From 5ee8b2fe5c75551d76447e39af7de26739ad1e36 Mon Sep 17 00:00:00 2001 From: Aaron Meyer Date: Sun, 21 Jun 2026 07:31:14 -0700 Subject: [PATCH 1/8] Repackaging RISE --- RISE/figures/common.py | 18 - RISE/tests/test_parafac2.py | 3 +- analysis/__init__.py | 1 + .../data/Thomson/ThomsonCellTypes.csv | 0 .../data/Thomson/ThomsonDoublets.csv | 0 {RISE => analysis}/data/Thomson/meta.csv | 0 .../data/lupus/ToppFun_Cmp14.csv | 0 analysis/figures/__init__.py | 1 + analysis/figures/common.py | 79 + analysis/figures/commonFuncs/__init__.py | 1 + .../figures/commonFuncs/plotLupus.py | 4 +- {RISE => analysis}/figures/figure2b_e.py | 3 +- {RISE => analysis}/figures/figure2f_h.py | 5 +- {RISE => analysis}/figures/figure3.py | 15 +- {RISE => analysis}/figures/figure4a_c.py | 0 {RISE => analysis}/figures/figure4d.py | 7 +- {RISE => analysis}/figures/figure4e_k.py | 11 +- {RISE => analysis}/figures/figure5a_e.py | 7 +- {RISE => analysis}/figures/figure5f_j.py | 3 +- {RISE => analysis}/figures/figure6.py | 0 {RISE => analysis}/figures/figureS10.py | 3 +- {RISE => analysis}/figures/figureS2.py | 6 +- {RISE => analysis}/figures/figureS3.py | 3 +- {RISE => analysis}/figures/figureS5.py | 3 +- {RISE => analysis}/figures/figureS6.py | 3 +- {RISE => analysis}/figures/figureS7.py | 5 +- {RISE => analysis}/figures/figureS8a_d.py | 0 {RISE => analysis}/figures/figureS8e_f.py | 3 +- {RISE => analysis}/figures/figureS8g_h.py | 11 +- {RISE => analysis}/figures/figureS9a_d.py | 2 +- {RISE => analysis}/figures/figureS9e_f.py | 9 +- {RISE => analysis}/gating.py | 4 +- {RISE => analysis}/imports.py | 12 +- {RISE => analysis}/logisticReg.py | 2 +- .../notebooks/lupus/Lupus_Annot.ipynb | 0 .../notebooks/thomson/Thomson_Annot.ipynb | 0 analysis/tests/__init__.py | 1 + {RISE => analysis}/tests/test_import.py | 2 +- docs/generate_tutorial_figures.py | 11 +- makefile | 21 +- pyproject.toml | 48 +- requirements-dev.lock | 275 -- requirements.lock | 275 -- uv.lock | 2612 ++++++++++------- 44 files changed, 1795 insertions(+), 1674 deletions(-) create mode 100644 analysis/__init__.py rename {RISE => analysis}/data/Thomson/ThomsonCellTypes.csv (100%) rename {RISE => analysis}/data/Thomson/ThomsonDoublets.csv (100%) rename {RISE => analysis}/data/Thomson/meta.csv (100%) rename {RISE => analysis}/data/lupus/ToppFun_Cmp14.csv (100%) create mode 100644 analysis/figures/__init__.py create mode 100644 analysis/figures/common.py create mode 100644 analysis/figures/commonFuncs/__init__.py rename {RISE => analysis}/figures/commonFuncs/plotLupus.py (97%) rename {RISE => analysis}/figures/figure2b_e.py (92%) rename {RISE => analysis}/figures/figure2f_h.py (96%) rename {RISE => analysis}/figures/figure3.py (96%) rename {RISE => analysis}/figures/figure4a_c.py (100%) rename {RISE => analysis}/figures/figure4d.py (89%) rename {RISE => analysis}/figures/figure4e_k.py (95%) rename {RISE => analysis}/figures/figure5a_e.py (90%) rename {RISE => analysis}/figures/figure5f_j.py (98%) rename {RISE => analysis}/figures/figure6.py (100%) rename {RISE => analysis}/figures/figureS10.py (85%) rename {RISE => analysis}/figures/figureS2.py (98%) rename {RISE => analysis}/figures/figureS3.py (93%) rename {RISE => analysis}/figures/figureS5.py (87%) rename {RISE => analysis}/figures/figureS6.py (85%) rename {RISE => analysis}/figures/figureS7.py (98%) rename {RISE => analysis}/figures/figureS8a_d.py (100%) rename {RISE => analysis}/figures/figureS8e_f.py (89%) rename {RISE => analysis}/figures/figureS8g_h.py (75%) rename {RISE => analysis}/figures/figureS9a_d.py (99%) rename {RISE => analysis}/figures/figureS9e_f.py (87%) rename {RISE => analysis}/gating.py (97%) rename {RISE => analysis}/imports.py (89%) rename {RISE => analysis}/logisticReg.py (98%) rename {RISE => analysis}/notebooks/lupus/Lupus_Annot.ipynb (100%) rename {RISE => analysis}/notebooks/thomson/Thomson_Annot.ipynb (100%) create mode 100644 analysis/tests/__init__.py rename {RISE => analysis}/tests/test_import.py (87%) delete mode 100644 requirements-dev.lock delete mode 100644 requirements.lock diff --git a/RISE/figures/common.py b/RISE/figures/common.py index f510e5b6..d53349be 100644 --- a/RISE/figures/common.py +++ b/RISE/figures/common.py @@ -2,8 +2,6 @@ This file contains functions that are used in multiple figures. """ -import sys -import time from string import ascii_letters import matplotlib @@ -61,19 +59,3 @@ def subplotLabel(axs: list[plt.Axes]): fontweight="bold", va="top", ) - - -def genFigure(): - """Main figure generation function.""" - start = time.time() - nameOut = "figure" + sys.argv[1] - - exec(f"from RISE.figures.{nameOut} import makeFigure", globals()) - ff = makeFigure() # type: ignore # noqa: F821 - - if ff is not None: - ff.savefig( - f"./output/{nameOut}.svg", dpi=300, bbox_inches="tight", pad_inches=0 - ) - - print(f"Figure {sys.argv[1]} is done after {time.time() - start} seconds.\n") diff --git a/RISE/tests/test_parafac2.py b/RISE/tests/test_parafac2.py index 2596b9ee..1af5c258 100644 --- a/RISE/tests/test_parafac2.py +++ b/RISE/tests/test_parafac2.py @@ -5,8 +5,9 @@ import numpy as np import pandas as pd +from analysis.imports import import_thomson + from ..factorization import pf2, rise_pca_r2x -from ..imports import import_thomson def test_factor_thomson_reprod(): diff --git a/analysis/__init__.py b/analysis/__init__.py new file mode 100644 index 00000000..cd0d3b9c --- /dev/null +++ b/analysis/__init__.py @@ -0,0 +1 @@ +"""Analysis package containing paper-specific datasets, gating, regression, and figure-generation scripts.""" diff --git a/RISE/data/Thomson/ThomsonCellTypes.csv b/analysis/data/Thomson/ThomsonCellTypes.csv similarity index 100% rename from RISE/data/Thomson/ThomsonCellTypes.csv rename to analysis/data/Thomson/ThomsonCellTypes.csv diff --git a/RISE/data/Thomson/ThomsonDoublets.csv b/analysis/data/Thomson/ThomsonDoublets.csv similarity index 100% rename from RISE/data/Thomson/ThomsonDoublets.csv rename to analysis/data/Thomson/ThomsonDoublets.csv diff --git a/RISE/data/Thomson/meta.csv b/analysis/data/Thomson/meta.csv similarity index 100% rename from RISE/data/Thomson/meta.csv rename to analysis/data/Thomson/meta.csv diff --git a/RISE/data/lupus/ToppFun_Cmp14.csv b/analysis/data/lupus/ToppFun_Cmp14.csv similarity index 100% rename from RISE/data/lupus/ToppFun_Cmp14.csv rename to analysis/data/lupus/ToppFun_Cmp14.csv diff --git a/analysis/figures/__init__.py b/analysis/figures/__init__.py new file mode 100644 index 00000000..ae774c5d --- /dev/null +++ b/analysis/figures/__init__.py @@ -0,0 +1 @@ +"""Figures subpackage for paper analysis.""" diff --git a/analysis/figures/common.py b/analysis/figures/common.py new file mode 100644 index 00000000..abeb1a61 --- /dev/null +++ b/analysis/figures/common.py @@ -0,0 +1,79 @@ +""" +This file contains functions that are used in multiple figures. +""" + +import sys +import time +from string import ascii_letters + +import matplotlib +import seaborn as sns +from matplotlib import gridspec +from matplotlib import pyplot as plt +from matplotlib.figure import Figure + +matplotlib.use("AGG") + +matplotlib.rcParams["legend.labelspacing"] = 0.2 +matplotlib.rcParams["legend.fontsize"] = 8 +matplotlib.rcParams["xtick.major.pad"] = 1.0 +matplotlib.rcParams["ytick.major.pad"] = 1.0 +matplotlib.rcParams["xtick.minor.pad"] = 0.9 +matplotlib.rcParams["ytick.minor.pad"] = 0.9 +matplotlib.rcParams["legend.handletextpad"] = 0.5 +matplotlib.rcParams["legend.handlelength"] = 0.5 +matplotlib.rcParams["legend.framealpha"] = 0.5 +matplotlib.rcParams["legend.markerscale"] = 0.7 +matplotlib.rcParams["legend.borderpad"] = 0.35 +matplotlib.rcParams["svg.fonttype"] = "none" + + +def getSetup( + figsize: tuple[float, float], gridd: tuple[int, int] +) -> tuple[list[plt.Axes], Figure]: + """Establish figure set-up with subplots.""" + sns.set_theme( + style="whitegrid", + font_scale=0.7, + color_codes=True, + palette="colorblind", + rc={"grid.linestyle": "dotted", "axes.linewidth": 0.6}, + ) + + # Setup plotting space and grid + f = plt.figure(figsize=figsize, layout="constrained") + gs1 = gridspec.GridSpec(gridd[0], gridd[1], figure=f) + + # Get list of axis objects + ax = [f.add_subplot(gs1[x]) for x in range(gridd[0] * gridd[1])] + + return ax, f + + +def subplotLabel(axs: list[plt.Axes]): + """Place subplot labels on figure.""" + for ii, ax in enumerate(axs): + ax.text( + -0.2, + 1.2, + ascii_letters[ii], + transform=ax.transAxes, + fontweight="bold", + va="top", + ) + + +def genFigure(): + """Main figure generation function.""" + start = time.time() + nameOut = "figure" + sys.argv[1] + + exec(f"from analysis.figures.{nameOut} import makeFigure", globals()) + ff = makeFigure() # type: ignore # noqa: F821 + + if ff is not None: + ff.savefig( + f"./output/{nameOut}.svg", dpi=300, bbox_inches="tight", pad_inches=0 + ) + + print(f"Figure {sys.argv[1]} is done after {time.time() - start} seconds.\n") diff --git a/analysis/figures/commonFuncs/__init__.py b/analysis/figures/commonFuncs/__init__.py new file mode 100644 index 00000000..d21e0485 --- /dev/null +++ b/analysis/figures/commonFuncs/__init__.py @@ -0,0 +1 @@ +"""Common functions and plotting utilities for figures.""" diff --git a/RISE/figures/commonFuncs/plotLupus.py b/analysis/figures/commonFuncs/plotLupus.py similarity index 97% rename from RISE/figures/commonFuncs/plotLupus.py rename to analysis/figures/commonFuncs/plotLupus.py index 9f95a363..e827c361 100644 --- a/RISE/figures/commonFuncs/plotLupus.py +++ b/analysis/figures/commonFuncs/plotLupus.py @@ -5,12 +5,12 @@ from matplotlib.axes import Axes from sklearn.metrics import RocCurveDisplay -from ...logisticReg import ( +from analysis.logisticReg import ( predaccuracy_lupus, predaccuracy_ranks_lupus, roc_lupus_fourtbatch, ) -from ..commonFuncs.plotGeneral import cell_count_perc_lupus_df +from RISE.figures.commonFuncs.plotGeneral import cell_count_perc_lupus_df def samples_only_lupus(X: anndata.AnnData): diff --git a/RISE/figures/figure2b_e.py b/analysis/figures/figure2b_e.py similarity index 92% rename from RISE/figures/figure2b_e.py rename to analysis/figures/figure2b_e.py index bb00fddd..60d3aeb4 100644 --- a/RISE/figures/figure2b_e.py +++ b/analysis/figures/figure2b_e.py @@ -7,8 +7,9 @@ import pacmap from sklearn.decomposition import PCA +from RISE.figures.commonFuncs.plotPaCMAP import plot_labels_pacmap + from .common import getSetup, subplotLabel -from .commonFuncs.plotPaCMAP import plot_labels_pacmap def makeFigure(): diff --git a/RISE/figures/figure2f_h.py b/analysis/figures/figure2f_h.py similarity index 96% rename from RISE/figures/figure2f_h.py rename to analysis/figures/figure2f_h.py index ec25ee3f..9f1ac87d 100644 --- a/RISE/figures/figure2f_h.py +++ b/analysis/figures/figure2f_h.py @@ -6,13 +6,14 @@ import numpy as np import pandas as pd -from .common import getSetup, subplotLabel -from .commonFuncs.plotFactors import ( +from RISE.figures.commonFuncs.plotFactors import ( plot_condition_factors, plot_eigenstate_factors, plot_gene_factors, ) +from .common import getSetup, subplotLabel + def makeFigure(): """Get a list of the axis objects and create a figure.""" diff --git a/RISE/figures/figure3.py b/analysis/figures/figure3.py similarity index 96% rename from RISE/figures/figure3.py rename to analysis/figures/figure3.py index ade0e8b4..5669a1ee 100644 --- a/RISE/figures/figure3.py +++ b/analysis/figures/figure3.py @@ -8,22 +8,23 @@ import seaborn as sns from matplotlib.axes import Axes -from .common import ( - getSetup, - subplotLabel, -) -from .commonFuncs.plotFactors import ( +from RISE.figures.commonFuncs.plotFactors import ( plot_condition_factors, plot_gene_factors, ) -from .commonFuncs.plotGeneral import ( +from RISE.figures.commonFuncs.plotGeneral import ( cell_count_perc_df, gene_plot_cells, plot_avegene_per_category, plot_avegene_per_celltype, plot_cell_gene_corr, ) -from .commonFuncs.plotPaCMAP import plot_labels_pacmap, plot_wp_pacmap +from RISE.figures.commonFuncs.plotPaCMAP import plot_labels_pacmap, plot_wp_pacmap + +from .common import ( + getSetup, + subplotLabel, +) from .figure2f_h import groupDrugs diff --git a/RISE/figures/figure4a_c.py b/analysis/figures/figure4a_c.py similarity index 100% rename from RISE/figures/figure4a_c.py rename to analysis/figures/figure4a_c.py diff --git a/RISE/figures/figure4d.py b/analysis/figures/figure4d.py similarity index 89% rename from RISE/figures/figure4d.py rename to analysis/figures/figure4d.py index 6aa4d713..ec82b2b5 100644 --- a/RISE/figures/figure4d.py +++ b/analysis/figures/figure4d.py @@ -12,10 +12,11 @@ from sklearn import preprocessing from sklearn.linear_model import LogisticRegression -from ..factorization import correct_conditions +from analysis.figures.commonFuncs.plotLupus import samples_only_lupus +from RISE.factorization import correct_conditions +from RISE.figures.commonFuncs.plotGeneral import rotate_xaxis, rotate_yaxis + from .common import getSetup, subplotLabel -from .commonFuncs.plotGeneral import rotate_xaxis, rotate_yaxis -from .commonFuncs.plotLupus import samples_only_lupus def makeFigure(): diff --git a/RISE/figures/figure4e_k.py b/analysis/figures/figure4e_k.py similarity index 95% rename from RISE/figures/figure4e_k.py rename to analysis/figures/figure4e_k.py index 49300be9..c681b966 100644 --- a/RISE/figures/figure4e_k.py +++ b/analysis/figures/figure4e_k.py @@ -9,14 +9,15 @@ from matplotlib.axes import Axes from scipy.stats import pearsonr -from .common import getSetup, subplotLabel -from .commonFuncs.plotFactors import plot_gene_factors -from .commonFuncs.plotGeneral import ( +from RISE.figures.commonFuncs.plotFactors import plot_gene_factors +from RISE.figures.commonFuncs.plotGeneral import ( avegene_per_status, cell_count_perc_lupus_df, rotate_xaxis, ) -from .commonFuncs.plotPaCMAP import plot_wp_pacmap +from RISE.figures.commonFuncs.plotPaCMAP import plot_wp_pacmap + +from .common import getSetup, subplotLabel def makeFigure(): @@ -155,7 +156,7 @@ def plot_ave2genes_per_status(df_total, gene1, gene2, ax): def plot_toppfun(ax): """Plot GSEA results""" - df = pd.read_csv("RISE/data/lupus/ToppFun_Cmp14.csv", dtype=str) + df = pd.read_csv("analysis/data/lupus/ToppFun_Cmp14.csv", dtype=str) df = df.drop(columns=["ID", "Verbose ID"]) category = df["Category"].to_numpy().astype(str) diff --git a/RISE/figures/figure5a_e.py b/analysis/figures/figure5a_e.py similarity index 90% rename from RISE/figures/figure5a_e.py rename to analysis/figures/figure5a_e.py index 827aa43b..f890b8a5 100644 --- a/RISE/figures/figure5a_e.py +++ b/analysis/figures/figure5a_e.py @@ -9,10 +9,11 @@ import seaborn as sns from matplotlib.axes import Axes +from RISE.figures.commonFuncs.plotFactors import plot_gene_factors +from RISE.figures.commonFuncs.plotGeneral import cell_count_perc_lupus_df, rotate_xaxis +from RISE.figures.commonFuncs.plotPaCMAP import plot_gene_pacmap, plot_wp_pacmap + from .common import getSetup, subplotLabel -from .commonFuncs.plotFactors import plot_gene_factors -from .commonFuncs.plotGeneral import cell_count_perc_lupus_df, rotate_xaxis -from .commonFuncs.plotPaCMAP import plot_gene_pacmap, plot_wp_pacmap from .figure4e_k import plot_correlation_cmp_cell_count_perc diff --git a/RISE/figures/figure5f_j.py b/analysis/figures/figure5f_j.py similarity index 98% rename from RISE/figures/figure5f_j.py rename to analysis/figures/figure5f_j.py index 84ef7288..0c335c5e 100644 --- a/RISE/figures/figure5f_j.py +++ b/analysis/figures/figure5f_j.py @@ -8,8 +8,9 @@ import seaborn as sns from matplotlib.axes import Axes +from RISE.figures.commonFuncs.plotPaCMAP import plot_wp_pacmap + from .common import getSetup, subplotLabel -from .commonFuncs.plotPaCMAP import plot_wp_pacmap def makeFigure(): diff --git a/RISE/figures/figure6.py b/analysis/figures/figure6.py similarity index 100% rename from RISE/figures/figure6.py rename to analysis/figures/figure6.py diff --git a/RISE/figures/figureS10.py b/analysis/figures/figureS10.py similarity index 85% rename from RISE/figures/figureS10.py rename to analysis/figures/figureS10.py index f22dc807..ba61c055 100644 --- a/RISE/figures/figureS10.py +++ b/analysis/figures/figureS10.py @@ -4,8 +4,9 @@ import anndata +from RISE.figures.commonFuncs.plotPaCMAP import plot_wp_pacmap + from .common import getSetup, subplotLabel -from .commonFuncs.plotPaCMAP import plot_wp_pacmap def makeFigure(): diff --git a/RISE/figures/figureS2.py b/analysis/figures/figureS2.py similarity index 98% rename from RISE/figures/figureS2.py rename to analysis/figures/figureS2.py index 1a8ee2a8..bd17ba2a 100644 --- a/RISE/figures/figureS2.py +++ b/analysis/figures/figureS2.py @@ -10,10 +10,10 @@ import scib from sklearn.decomposition import PCA -from .common import getSetup, subplotLabel - # from .commonFuncs.plotGeneral import plot_r2x -from .commonFuncs.plotPaCMAP import plot_labels_pacmap +from RISE.figures.commonFuncs.plotPaCMAP import plot_labels_pacmap + +from .common import getSetup, subplotLabel # import seaborn as sns diff --git a/RISE/figures/figureS3.py b/analysis/figures/figureS3.py similarity index 93% rename from RISE/figures/figureS3.py rename to analysis/figures/figureS3.py index e3fb21cf..25143806 100644 --- a/RISE/figures/figureS3.py +++ b/analysis/figures/figureS3.py @@ -6,8 +6,9 @@ import seaborn as sns from matplotlib.axes import Axes +from RISE.figures.commonFuncs.plotGeneral import cell_count_perc_df, rotate_xaxis + from .common import getSetup, subplotLabel -from .commonFuncs.plotGeneral import cell_count_perc_df, rotate_xaxis def makeFigure(): diff --git a/RISE/figures/figureS5.py b/analysis/figures/figureS5.py similarity index 87% rename from RISE/figures/figureS5.py rename to analysis/figures/figureS5.py index 50f7d7d8..dd36f834 100644 --- a/RISE/figures/figureS5.py +++ b/analysis/figures/figureS5.py @@ -5,8 +5,9 @@ import anndata import seaborn as sns +from RISE.figures.commonFuncs.plotGeneral import cell_count_perc_df, rotate_xaxis + from .common import getSetup, subplotLabel -from .commonFuncs.plotGeneral import cell_count_perc_df, rotate_xaxis def makeFigure(): diff --git a/RISE/figures/figureS6.py b/analysis/figures/figureS6.py similarity index 85% rename from RISE/figures/figureS6.py rename to analysis/figures/figureS6.py index 29c87271..e14f1c77 100644 --- a/RISE/figures/figureS6.py +++ b/analysis/figures/figureS6.py @@ -4,8 +4,9 @@ import anndata +from RISE.figures.commonFuncs.plotPaCMAP import plot_labels_pacmap, plot_wp_pacmap + from .common import getSetup, subplotLabel -from .commonFuncs.plotPaCMAP import plot_labels_pacmap, plot_wp_pacmap def makeFigure(): diff --git a/RISE/figures/figureS7.py b/analysis/figures/figureS7.py similarity index 98% rename from RISE/figures/figureS7.py rename to analysis/figures/figureS7.py index d65b42a2..40cb2dde 100644 --- a/RISE/figures/figureS7.py +++ b/analysis/figures/figureS7.py @@ -9,8 +9,9 @@ from matplotlib.axes import Axes from scipy.stats import linregress -from ..factorization import pf2 -from ..imports import import_thomson +from analysis.imports import import_thomson +from RISE.factorization import pf2 + from .common import getSetup, subplotLabel diff --git a/RISE/figures/figureS8a_d.py b/analysis/figures/figureS8a_d.py similarity index 100% rename from RISE/figures/figureS8a_d.py rename to analysis/figures/figureS8a_d.py diff --git a/RISE/figures/figureS8e_f.py b/analysis/figures/figureS8e_f.py similarity index 89% rename from RISE/figures/figureS8e_f.py rename to analysis/figures/figureS8e_f.py index 1566a26f..791fe65e 100644 --- a/RISE/figures/figureS8e_f.py +++ b/analysis/figures/figureS8e_f.py @@ -4,8 +4,9 @@ import anndata +from analysis.figures.commonFuncs.plotLupus import plot_roc_fourthbatch + from .common import getSetup, subplotLabel -from .commonFuncs.plotLupus import plot_roc_fourthbatch def makeFigure(): diff --git a/RISE/figures/figureS8g_h.py b/analysis/figures/figureS8g_h.py similarity index 75% rename from RISE/figures/figureS8g_h.py rename to analysis/figures/figureS8g_h.py index 42c86f28..93d45a1b 100644 --- a/RISE/figures/figureS8g_h.py +++ b/analysis/figures/figureS8g_h.py @@ -4,15 +4,16 @@ import anndata -from ..factorization import correct_conditions -from .common import getSetup, subplotLabel -from .commonFuncs.plotFactors import ( +from analysis.figures.commonFuncs.plotLupus import samples_only_lupus +from RISE.factorization import correct_conditions +from RISE.figures.commonFuncs.plotFactors import ( plot_condition_factors, plot_eigenstate_factors, plot_gene_factors, ) -from .commonFuncs.plotLupus import samples_only_lupus -from .commonFuncs.plotPaCMAP import plot_labels_pacmap +from RISE.figures.commonFuncs.plotPaCMAP import plot_labels_pacmap + +from .common import getSetup, subplotLabel def makeFigure(): diff --git a/RISE/figures/figureS9a_d.py b/analysis/figures/figureS9a_d.py similarity index 99% rename from RISE/figures/figureS9a_d.py rename to analysis/figures/figureS9a_d.py index 49c790e9..dcac8f8d 100644 --- a/RISE/figures/figureS9a_d.py +++ b/analysis/figures/figureS9a_d.py @@ -19,9 +19,9 @@ from harmonypy import run_harmony from scipy.sparse import csr_array +from analysis.imports import import_lupus from RISE.factorization import pf2 from RISE.figures.common import getSetup, subplotLabel -from RISE.imports import import_lupus # Simplified to single-line comments for configuration flags RECOMPUTE = False diff --git a/RISE/figures/figureS9e_f.py b/analysis/figures/figureS9e_f.py similarity index 87% rename from RISE/figures/figureS9e_f.py rename to analysis/figures/figureS9e_f.py index 357de5f8..68243ae4 100644 --- a/RISE/figures/figureS9e_f.py +++ b/analysis/figures/figureS9e_f.py @@ -8,11 +8,12 @@ import seaborn as sns from matplotlib.axes import Axes -from ..factorization import correct_conditions -from ..logisticReg import logistic_regression +from analysis.figures.commonFuncs.plotLupus import samples_only_lupus +from analysis.logisticReg import logistic_regression +from RISE.factorization import correct_conditions +from RISE.figures.commonFuncs.plotGeneral import cell_count_perc_lupus_df, rotate_xaxis + from .common import getSetup, subplotLabel -from .commonFuncs.plotGeneral import cell_count_perc_lupus_df, rotate_xaxis -from .commonFuncs.plotLupus import samples_only_lupus def makeFigure(): diff --git a/RISE/gating.py b/analysis/gating.py similarity index 97% rename from RISE/gating.py rename to analysis/gating.py index 7318cdd4..eb2c2cd1 100644 --- a/RISE/gating.py +++ b/analysis/gating.py @@ -17,7 +17,7 @@ def gateThomsonCellsLeiden(X) -> npt.ArrayLike: def gateThomsonCells(X) -> npt.ArrayLike: """Manually gates cell types for Thomson PaCMAP""" - cellTypeDF = pd.read_csv("RISE/data/Thomson/ThomsonCellTypes.csv", index_col=0) + cellTypeDF = pd.read_csv("analysis/data/Thomson/ThomsonCellTypes.csv", index_col=0) cellTypeDF.index.name = "cell_barcode" X.obs = X.obs.join(cellTypeDF, on="cell_barcode", how="inner") @@ -42,7 +42,7 @@ def Thomson_Doublet(): doublet_score = clf.doublet_score() X.obs["doublet"] = doublets X.obs["doublet_score"] = doublet_score - X.obs["doublet"].to_csv("RISE/data/Thomson/ThomsonDoublets.csv") + X.obs["doublet"].to_csv("analysis/data/Thomson/ThomsonDoublets.csv") def getHiResOldLupus(X) -> npt.ArrayLike: diff --git a/RISE/imports.py b/analysis/imports.py similarity index 89% rename from RISE/imports.py rename to analysis/imports.py index 4c28fa89..c01a5c6b 100644 --- a/RISE/imports.py +++ b/analysis/imports.py @@ -1,5 +1,6 @@ import anndata import pandas as pd +import scanpy as sc from parafac2.normalize import prepare_dataset from .gating import gateThomsonCells @@ -8,11 +9,10 @@ def import_thomson() -> anndata.AnnData: """Import Thompson lab PBMC dataset.""" # Cell barcodes, sample id of treatment and sample number - metafile = pd.read_csv("RISE/data/Thomson/meta.csv", usecols=[0, 1]) - # X = sc.read_10x_mtx( - # "/opt/andrew/Thomson/", var_names="gene_symbols", make_unique=True - # ) - X = anndata.read_h5ad("/opt/andrew/thomson_raw.h5ad") + metafile = pd.read_csv("analysis/data/Thomson/meta.csv", usecols=[0, 1]) + X = sc.read_10x_mtx( + "/opt/andrew/Thomson/", var_names="gene_symbols", make_unique=True + ) obs = X.obs.reset_index(names="cell_barcode") metafile = pd.merge( @@ -26,7 +26,7 @@ def import_thomson() -> anndata.AnnData: } ) - doubletDF = pd.read_csv("RISE/data/Thomson/ThomsonDoublets.csv", index_col=0) + doubletDF = pd.read_csv("analysis/data/Thomson/ThomsonDoublets.csv", index_col=0) doubletDF.index.name = "cell_barcode" X.obs = X.obs.join(doubletDF, on="cell_barcode", how="inner") diff --git a/RISE/logisticReg.py b/analysis/logisticReg.py similarity index 98% rename from RISE/logisticReg.py rename to analysis/logisticReg.py index 7c065c12..a709f0b2 100644 --- a/RISE/logisticReg.py +++ b/analysis/logisticReg.py @@ -5,7 +5,7 @@ from sklearn.metrics import roc_auc_score from sklearn.utils import resample -from .factorization import correct_conditions, pf2 +from RISE.factorization import correct_conditions, pf2 def predaccuracy_ranks_lupus( diff --git a/RISE/notebooks/lupus/Lupus_Annot.ipynb b/analysis/notebooks/lupus/Lupus_Annot.ipynb similarity index 100% rename from RISE/notebooks/lupus/Lupus_Annot.ipynb rename to analysis/notebooks/lupus/Lupus_Annot.ipynb diff --git a/RISE/notebooks/thomson/Thomson_Annot.ipynb b/analysis/notebooks/thomson/Thomson_Annot.ipynb similarity index 100% rename from RISE/notebooks/thomson/Thomson_Annot.ipynb rename to analysis/notebooks/thomson/Thomson_Annot.ipynb diff --git a/analysis/tests/__init__.py b/analysis/tests/__init__.py new file mode 100644 index 00000000..ce19cf19 --- /dev/null +++ b/analysis/tests/__init__.py @@ -0,0 +1 @@ +"""Tests package for analysis.""" diff --git a/RISE/tests/test_import.py b/analysis/tests/test_import.py similarity index 87% rename from RISE/tests/test_import.py rename to analysis/tests/test_import.py index a9821e3c..5ddeeda2 100644 --- a/RISE/tests/test_import.py +++ b/analysis/tests/test_import.py @@ -5,7 +5,7 @@ import numpy as np import pytest -from ..imports import import_lupus, import_thomson +from analysis.imports import import_thomson @pytest.mark.parametrize( diff --git a/docs/generate_tutorial_figures.py b/docs/generate_tutorial_figures.py index cba5dbdd..d10a6767 100644 --- a/docs/generate_tutorial_figures.py +++ b/docs/generate_tutorial_figures.py @@ -3,28 +3,29 @@ import matplotlib matplotlib.use("Agg") # Non-interactive backend -import matplotlib.pyplot as plt from pathlib import Path +import matplotlib.pyplot as plt + # Create output directory output_dir = Path(__file__).parent / "_static" / "tutorial_images" output_dir.mkdir(parents=True, exist_ok=True) # Import RISE modules -from RISE.imports import import_thomson -from RISE.figures.commonFuncs.plotGeneral import plot_r2x -from RISE.figures.figureS4 import plot_fms_diff_ranks +from analysis.imports import import_thomson from RISE.factorization import pf2 from RISE.figures.commonFuncs.plotFactors import ( plot_condition_factors, plot_eigenstate_factors, plot_gene_factors, ) +from RISE.figures.commonFuncs.plotGeneral import plot_r2x from RISE.figures.commonFuncs.plotPaCMAP import ( - plot_labels_pacmap, plot_gene_pacmap, + plot_labels_pacmap, plot_wp_pacmap, ) +from RISE.figures.figureS4 import plot_fms_diff_ranks print("Loading dataset...") X = import_thomson() diff --git a/makefile b/makefile index 378a859a..ce4b7e18 100644 --- a/makefile +++ b/makefile @@ -1,20 +1,16 @@ -.PHONY: clean test pyright +.PHONY: clean test ty -flist = $(wildcard RISE/figures/figure*.py) -allOutput = $(patsubst RISE/figures/figure%.py, output/figure%.svg, $(flist)) +flist = $(wildcard analysis/figures/figure*.py) +allOutput = $(patsubst analysis/figures/figure%.py, output/figure%.svg, $(flist)) all: $(allOutput) -allThomson: $(filter output/figureThomson%, $(allOutput)) - -allLupus: $(filter output/figureLupus%, $(allOutput)) - -output/figure%.svg: RISE/figures/figure%.py +output/figure%.svg: analysis/figures/figure%.py @ mkdir -p ./output uv run fbuild $* test: .venv - uv run pytest -s -v -x + uv run pytest -s -v .venv: pyproject.toml uv sync @@ -22,9 +18,8 @@ test: .venv coverage.xml: .venv uv run pytest --junitxml=junit.xml --cov=RISE --cov-report xml:coverage.xml -pyright: .venv - uv run pyright RISE +ty: .venv + uv run ty check RISE analysis clean: - rm -rf output profile profile.svg - rm -rf factor_cache + rm -rf output profile profile.svg factor_cache diff --git a/pyproject.toml b/pyproject.toml index 81202071..316de765 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,52 +4,58 @@ version = "0.1.0" description = "Single cell analysis across conditions using PARAFAC2." authors = [{name = "Andrew Ramirez"}, {name = "Aaron Meyer", email = "git@asmlab.org" }] license = "MIT" -requires-python = ">= 3.12" +requires-python = ">= 3.13" dependencies = [ "numpy>=2.2", "scipy>=1.16", "scikit-learn>=1.6", - "seaborn>=0.13.2", "pandas>=2.2.1", "tensorly>=0.8.1", - "parafac2 @ git+https://github.com/meyer-lab/parafac2.git@ccf708fe71c78a106151643e893ea006bba865d9", - "h5netcdf>=1.3", + "parafac2 @ git+https://github.com/meyer-lab/parafac2.git@v1.2.0", "anndata>=0.10.3", - "datashader>=0.16", - "gseapy>=1.1", - "scanpy>=1.11", "pacmap>=0.7.1", "tqdm>=4.66.1", - "tlviz>=0.1.1", - "doubletdetection>=4.3", - "statsmodels>=0.14.1", - "dask[dataframe]>=2024.3.1", - "ortools>=9.12.4544", - "fmt>=0.3.1", ] readme = "README.md" [project.scripts] -fbuild = "RISE.figures.common:genFigure" -factor = "RISE.imports:factorSave" +fbuild = "analysis.figures.common:genFigure" +factor = "analysis.imports:factorSave" [build-system] requires = ["hatchling"] build-backend = "hatchling.build" [dependency-groups] -dev = [ - "pytest>=9.0", - "pytest-cov>=7.0", - "pyright>=1.1.407", +analysis = [ + "seaborn>=0.13.2", + "h5netcdf>=1.3", + "datashader>=0.16", + "gseapy>=1.1", + "scanpy>=1.11", + "tlviz>=0.1.1", + "doubletdetection>=4.3", + "statsmodels>=0.14.1", + "dask[dataframe]>=2024.3.1", + "ortools>=9.12.4544", + "fmt>=0.3.1", "scanorama>=1.7.4", "harmonypy>=0.0.10", "scib>=1.1.5", - "sphinx>=7.0,<9.0", +] +docs = [ + { include-group = "analysis" }, + "sphinx>=9.0", "sphinx-rtd-theme>=3.0.0", "nbsphinx>=0.9.0", +] +dev = [ + { include-group = "analysis" }, + "pytest>=9.0", + "pytest-cov>=7.0", + "ty", "ruff>=0.14.7", ] @@ -57,7 +63,7 @@ dev = [ allow-direct-references = true [tool.hatch.build.targets.wheel] -packages = ["RISE"] +packages = ["RISE", "analysis"] [tool.ruff.lint] select = [ diff --git a/requirements-dev.lock b/requirements-dev.lock deleted file mode 100644 index b5a0baf7..00000000 --- a/requirements-dev.lock +++ /dev/null @@ -1,275 +0,0 @@ -# generated by rye -# use `rye lock` or `rye sync` to update this lockfile -# -# last locked with the following flags: -# pre: false -# features: [] -# all-features: false -# with-sources: false -# generate-hashes: false -# universal: false - --e file:. -absl-py==2.3.1 - # via ortools -anndata==0.12.6 - # via doubletdetection - # via parafac2 - # via rise - # via scanpy -annoy==1.17.3 - # via pacmap -array-api-compat==1.12.0 - # via anndata -certifi==2025.11.12 - # via requests -charset-normalizer==3.4.4 - # via requests -click==8.3.1 - # via dask -cloudpickle==3.1.2 - # via dask -colorcet==3.1.0 - # via datashader -contourpy==1.3.3 - # via matplotlib -cupy-cuda12x==13.6.0 - # via parafac2 -cycler==0.12.1 - # via matplotlib -dask==2025.11.0 - # via rise -datashader==0.18.2 - # via rise -donfig==0.8.1.post1 - # via zarr -doubletdetection==4.3.0.post1 - # via rise -fastrlock==0.8.3 - # via cupy-cuda12x -fmt==0.3.1 - # via rise -fonttools==4.61.0 - # via matplotlib -fsspec==2025.12.0 - # via dask -google-crc32c==1.7.1 - # via zarr -gseapy==1.1.11 - # via rise -h5netcdf==1.7.3 - # via rise -h5py==3.15.1 - # via anndata - # via h5netcdf - # via scanpy -idna==3.11 - # via requests -igraph==1.0.0 - # via leidenalg -immutabledict==4.2.2 - # via ortools -joblib==1.5.2 - # via pynndescent - # via scanpy - # via scikit-learn -kiwisolver==1.4.9 - # via matplotlib -legacy-api-wrap==1.5 - # via anndata - # via scanpy -leidenalg==0.11.0 - # via phenograph -llvmlite==0.46.0 - # via numba - # via pynndescent -locket==1.0.0 - # via partd -matplotlib==3.10.7 - # via doubletdetection - # via gseapy - # via scanpy - # via seaborn - # via tlviz -multipledispatch==1.0.0 - # via datashader -natsort==8.4.0 - # via anndata - # via scanpy -networkx==3.6.1 - # via scanpy -numba==0.63.1 - # via datashader - # via pacmap - # via pynndescent - # via scanpy - # via umap-learn -numcodecs==0.16.5 - # via zarr -numpy==2.3.5 - # via anndata - # via contourpy - # via cupy-cuda12x - # via dask - # via datashader - # via doubletdetection - # via gseapy - # via h5py - # via matplotlib - # via numba - # via numcodecs - # via ortools - # via pacmap - # via pandas - # via parafac2 - # via patsy - # via phenograph - # via rise - # via scanpy - # via scikit-learn - # via scipy - # via seaborn - # via statsmodels - # via tensorly - # via tlviz - # via umap-learn - # via xarray - # via zarr -ortools==9.14.6206 - # via rise -packaging==25.0 - # via anndata - # via dask - # via datashader - # via h5netcdf - # via matplotlib - # via scanpy - # via statsmodels - # via xarray - # via zarr -pacmap==0.8.0 - # via rise -pandas==2.3.3 - # via anndata - # via dask - # via datashader - # via gseapy - # via ortools - # via rise - # via scanpy - # via seaborn - # via statsmodels - # via tlviz - # via xarray -parafac2 @ git+https://github.com/meyer-lab/parafac2.git@ccf708fe71c78a106151643e893ea006bba865d9 - # via rise -param==2.3.1 - # via datashader - # via pyct -partd==1.4.2 - # via dask -patsy==1.0.2 - # via scanpy - # via statsmodels -phenograph==1.5.7 - # via doubletdetection -pillow==12.0.0 - # via matplotlib -protobuf==6.31.1 - # via ortools -psutil==7.1.3 - # via phenograph -pyarrow==22.0.0 - # via dask -pyct==0.6.0 - # via datashader -pynndescent==0.5.13 - # via scanpy - # via umap-learn -pyparsing==3.2.5 - # via matplotlib -python-dateutil==2.9.0.post0 - # via matplotlib - # via pandas -pytz==2025.2 - # via pandas -pyyaml==6.0.3 - # via dask - # via donfig -requests==2.32.5 - # via datashader - # via gseapy - # via tlviz -scanpy==1.11.5 - # via doubletdetection - # via rise -scikit-learn==1.8.0 - # via pacmap - # via phenograph - # via pynndescent - # via rise - # via scanpy - # via umap-learn -scipy==1.16.3 - # via anndata - # via datashader - # via doubletdetection - # via gseapy - # via parafac2 - # via phenograph - # via pynndescent - # via rise - # via scanpy - # via scikit-learn - # via statsmodels - # via tensorly - # via tlviz - # via umap-learn -seaborn==0.13.2 - # via rise - # via scanpy -session-info2==0.2.3 - # via scanpy -setuptools==80.9.0 - # via phenograph -six==1.17.0 - # via python-dateutil -statsmodels==0.14.6 - # via rise - # via scanpy - # via tlviz -tensorly==0.9.0 - # via parafac2 - # via rise -texttable==1.7.0 - # via igraph -threadpoolctl==3.6.0 - # via scikit-learn -tlviz==0.1.1 - # via rise -toolz==1.1.0 - # via dask - # via datashader - # via partd -tqdm==4.67.1 - # via doubletdetection - # via parafac2 - # via rise - # via scanpy - # via umap-learn -typing-extensions==4.15.0 - # via numcodecs - # via ortools - # via scanpy - # via zarr -tzdata==2025.2 - # via pandas -umap-learn==0.5.9.post2 - # via scanpy -urllib3==2.6.1 - # via requests -xarray==2025.12.0 - # via datashader - # via tlviz -zarr==3.1.5 - # via anndata diff --git a/requirements.lock b/requirements.lock deleted file mode 100644 index b5a0baf7..00000000 --- a/requirements.lock +++ /dev/null @@ -1,275 +0,0 @@ -# generated by rye -# use `rye lock` or `rye sync` to update this lockfile -# -# last locked with the following flags: -# pre: false -# features: [] -# all-features: false -# with-sources: false -# generate-hashes: false -# universal: false - --e file:. -absl-py==2.3.1 - # via ortools -anndata==0.12.6 - # via doubletdetection - # via parafac2 - # via rise - # via scanpy -annoy==1.17.3 - # via pacmap -array-api-compat==1.12.0 - # via anndata -certifi==2025.11.12 - # via requests -charset-normalizer==3.4.4 - # via requests -click==8.3.1 - # via dask -cloudpickle==3.1.2 - # via dask -colorcet==3.1.0 - # via datashader -contourpy==1.3.3 - # via matplotlib -cupy-cuda12x==13.6.0 - # via parafac2 -cycler==0.12.1 - # via matplotlib -dask==2025.11.0 - # via rise -datashader==0.18.2 - # via rise -donfig==0.8.1.post1 - # via zarr -doubletdetection==4.3.0.post1 - # via rise -fastrlock==0.8.3 - # via cupy-cuda12x -fmt==0.3.1 - # via rise -fonttools==4.61.0 - # via matplotlib -fsspec==2025.12.0 - # via dask -google-crc32c==1.7.1 - # via zarr -gseapy==1.1.11 - # via rise -h5netcdf==1.7.3 - # via rise -h5py==3.15.1 - # via anndata - # via h5netcdf - # via scanpy -idna==3.11 - # via requests -igraph==1.0.0 - # via leidenalg -immutabledict==4.2.2 - # via ortools -joblib==1.5.2 - # via pynndescent - # via scanpy - # via scikit-learn -kiwisolver==1.4.9 - # via matplotlib -legacy-api-wrap==1.5 - # via anndata - # via scanpy -leidenalg==0.11.0 - # via phenograph -llvmlite==0.46.0 - # via numba - # via pynndescent -locket==1.0.0 - # via partd -matplotlib==3.10.7 - # via doubletdetection - # via gseapy - # via scanpy - # via seaborn - # via tlviz -multipledispatch==1.0.0 - # via datashader -natsort==8.4.0 - # via anndata - # via scanpy -networkx==3.6.1 - # via scanpy -numba==0.63.1 - # via datashader - # via pacmap - # via pynndescent - # via scanpy - # via umap-learn -numcodecs==0.16.5 - # via zarr -numpy==2.3.5 - # via anndata - # via contourpy - # via cupy-cuda12x - # via dask - # via datashader - # via doubletdetection - # via gseapy - # via h5py - # via matplotlib - # via numba - # via numcodecs - # via ortools - # via pacmap - # via pandas - # via parafac2 - # via patsy - # via phenograph - # via rise - # via scanpy - # via scikit-learn - # via scipy - # via seaborn - # via statsmodels - # via tensorly - # via tlviz - # via umap-learn - # via xarray - # via zarr -ortools==9.14.6206 - # via rise -packaging==25.0 - # via anndata - # via dask - # via datashader - # via h5netcdf - # via matplotlib - # via scanpy - # via statsmodels - # via xarray - # via zarr -pacmap==0.8.0 - # via rise -pandas==2.3.3 - # via anndata - # via dask - # via datashader - # via gseapy - # via ortools - # via rise - # via scanpy - # via seaborn - # via statsmodels - # via tlviz - # via xarray -parafac2 @ git+https://github.com/meyer-lab/parafac2.git@ccf708fe71c78a106151643e893ea006bba865d9 - # via rise -param==2.3.1 - # via datashader - # via pyct -partd==1.4.2 - # via dask -patsy==1.0.2 - # via scanpy - # via statsmodels -phenograph==1.5.7 - # via doubletdetection -pillow==12.0.0 - # via matplotlib -protobuf==6.31.1 - # via ortools -psutil==7.1.3 - # via phenograph -pyarrow==22.0.0 - # via dask -pyct==0.6.0 - # via datashader -pynndescent==0.5.13 - # via scanpy - # via umap-learn -pyparsing==3.2.5 - # via matplotlib -python-dateutil==2.9.0.post0 - # via matplotlib - # via pandas -pytz==2025.2 - # via pandas -pyyaml==6.0.3 - # via dask - # via donfig -requests==2.32.5 - # via datashader - # via gseapy - # via tlviz -scanpy==1.11.5 - # via doubletdetection - # via rise -scikit-learn==1.8.0 - # via pacmap - # via phenograph - # via pynndescent - # via rise - # 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("https://docs.python.org/3", None), @@ -80,7 +77,7 @@ "pandas": ("https://pandas.pydata.org/docs/", None), "anndata": ("https://anndata.readthedocs.io/en/stable/", None), "sklearn": ("https://scikit-learn.org/stable/", None), - "tensorly": ("http://tensorly.org/stable/", None), + "tensorly": ("https://tensorly.org/stable/", None), "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None), } diff --git a/pyproject.toml b/pyproject.toml index 316de765..cf718297 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,7 +49,7 @@ docs = [ { include-group = "analysis" }, "sphinx>=9.0", "sphinx-rtd-theme>=3.0.0", - "nbsphinx>=0.9.0", + "nbsphinx>=0.9", ] dev = [ { include-group = "analysis" }, From 565845ce681e5d2d9730c6f591c64f78c299fa47 Mon Sep 17 00:00:00 2001 From: Aaron Meyer Date: Sun, 21 Jun 2026 07:42:09 -0700 Subject: [PATCH 3/8] Refactor plotting code --- RISE/figures/__init__.py | 1 - RISE/figures/common.py | 61 ------------------- RISE/figures/commonFuncs/__init__.py | 1 - RISE/plotting/__init__.py | 53 ++++++++++++++++ .../plotFactors.py => plotting/factors.py} | 0 .../plotGeneral.py => plotting/general.py} | 2 +- .../plotPaCMAP.py => plotting/pacmap.py} | 6 +- .../commonFuncs => plotting}/seriate.py | 0 .../figureS4.py => plotting/stability.py} | 23 +------ analysis/figures/commonFuncs/plotLupus.py | 2 +- analysis/figures/figure2b_e.py | 2 +- analysis/figures/figure2f_h.py | 2 +- analysis/figures/figure3.py | 11 ++-- analysis/figures/figure4d.py | 2 +- analysis/figures/figure4e_k.py | 6 +- analysis/figures/figure5a_e.py | 10 ++- analysis/figures/figure5f_j.py | 2 +- analysis/figures/figureS10.py | 2 +- analysis/figures/figureS2.py | 4 +- analysis/figures/figureS3.py | 2 +- analysis/figures/figureS4.py | 19 ++++++ analysis/figures/figureS5.py | 2 +- analysis/figures/figureS6.py | 2 +- analysis/figures/figureS8g_h.py | 4 +- analysis/figures/figureS9a_d.py | 3 +- analysis/figures/figureS9e_f.py | 2 +- docs/api.rst | 16 ++--- docs/generate_tutorial_figures.py | 8 +-- docs/tutorial.rst | 18 +++--- makefile | 4 +- 30 files changed, 133 insertions(+), 137 deletions(-) delete mode 100644 RISE/figures/__init__.py delete mode 100644 RISE/figures/common.py delete mode 100644 RISE/figures/commonFuncs/__init__.py create mode 100644 RISE/plotting/__init__.py rename RISE/{figures/commonFuncs/plotFactors.py => plotting/factors.py} (100%) rename RISE/{figures/commonFuncs/plotGeneral.py => plotting/general.py} (99%) rename RISE/{figures/commonFuncs/plotPaCMAP.py => plotting/pacmap.py} (97%) rename RISE/{figures/commonFuncs => plotting}/seriate.py (100%) rename RISE/{figures/figureS4.py => plotting/stability.py} (91%) create mode 100644 analysis/figures/figureS4.py diff --git a/RISE/figures/__init__.py b/RISE/figures/__init__.py deleted file mode 100644 index 4e0307ef..00000000 --- a/RISE/figures/__init__.py +++ /dev/null @@ -1 +0,0 @@ -"""RISE figure generation modules.""" diff --git a/RISE/figures/common.py b/RISE/figures/common.py deleted file mode 100644 index d53349be..00000000 --- a/RISE/figures/common.py +++ /dev/null @@ -1,61 +0,0 @@ -""" -This file contains functions that are used in multiple figures. -""" - -from string import ascii_letters - -import matplotlib -import seaborn as sns -from matplotlib import gridspec -from matplotlib import pyplot as plt -from matplotlib.figure import Figure - -matplotlib.use("AGG") - -matplotlib.rcParams["legend.labelspacing"] = 0.2 -matplotlib.rcParams["legend.fontsize"] = 8 -matplotlib.rcParams["xtick.major.pad"] = 1.0 -matplotlib.rcParams["ytick.major.pad"] = 1.0 -matplotlib.rcParams["xtick.minor.pad"] = 0.9 -matplotlib.rcParams["ytick.minor.pad"] = 0.9 -matplotlib.rcParams["legend.handletextpad"] = 0.5 -matplotlib.rcParams["legend.handlelength"] = 0.5 -matplotlib.rcParams["legend.framealpha"] = 0.5 -matplotlib.rcParams["legend.markerscale"] = 0.7 -matplotlib.rcParams["legend.borderpad"] = 0.35 -matplotlib.rcParams["svg.fonttype"] = "none" - - -def getSetup( - figsize: tuple[float, float], gridd: tuple[int, int] -) -> tuple[list[plt.Axes], Figure]: - """Establish figure set-up with subplots.""" - sns.set_theme( - style="whitegrid", - font_scale=0.7, - color_codes=True, - palette="colorblind", - rc={"grid.linestyle": "dotted", "axes.linewidth": 0.6}, - ) - - # Setup plotting space and grid - f = plt.figure(figsize=figsize, layout="constrained") - gs1 = gridspec.GridSpec(gridd[0], gridd[1], figure=f) - - # Get list of axis objects - ax = [f.add_subplot(gs1[x]) for x in range(gridd[0] * gridd[1])] - - return ax, f - - -def subplotLabel(axs: list[plt.Axes]): - """Place subplot labels on figure.""" - for ii, ax in enumerate(axs): - ax.text( - -0.2, - 1.2, - ascii_letters[ii], - transform=ax.transAxes, - fontweight="bold", - va="top", - ) diff --git a/RISE/figures/commonFuncs/__init__.py b/RISE/figures/commonFuncs/__init__.py deleted file mode 100644 index cdc74d0b..00000000 --- a/RISE/figures/commonFuncs/__init__.py +++ /dev/null @@ -1 +0,0 @@ -"""Common functions for RISE figure generation.""" diff --git a/RISE/plotting/__init__.py b/RISE/plotting/__init__.py new file mode 100644 index 00000000..8edf6be6 --- /dev/null +++ b/RISE/plotting/__init__.py @@ -0,0 +1,53 @@ +""" +Plotting and visualization functions for RISE. +""" + +from .factors import ( + plot_condition_factors, + plot_eigenstate_factors, + plot_gene_factors, +) +from .general import ( + avegene_per_status, + cell_count_perc_df, + cell_count_perc_lupus_df, + gene_plot_cells, + plot_avegene_per_category, + plot_avegene_per_celltype, + plot_cell_gene_corr, + plot_r2x, + rotate_xaxis, + rotate_yaxis, +) +from .pacmap import ( + plot_gene_pacmap, + plot_labels_pacmap, + plot_wp_pacmap, +) +from .stability import ( + calculateFMS, + plot_fms_diff_ranks, + plot_fms_percent_drop, +) + +__all__ = [ + "plot_condition_factors", + "plot_eigenstate_factors", + "plot_gene_factors", + "avegene_per_status", + "cell_count_perc_df", + "cell_count_perc_lupus_df", + "gene_plot_cells", + "plot_avegene_per_category", + "plot_avegene_per_celltype", + "plot_cell_gene_corr", + "plot_r2x", + "rotate_xaxis", + "rotate_yaxis", + "plot_gene_pacmap", + "plot_labels_pacmap", + "plot_wp_pacmap", + "calculateFMS", + "plot_fms_diff_ranks", + "plot_fms_percent_drop", +] diff --git a/RISE/figures/commonFuncs/plotFactors.py b/RISE/plotting/factors.py similarity index 100% rename from RISE/figures/commonFuncs/plotFactors.py rename to RISE/plotting/factors.py diff --git a/RISE/figures/commonFuncs/plotGeneral.py b/RISE/plotting/general.py similarity index 99% rename from RISE/figures/commonFuncs/plotGeneral.py rename to RISE/plotting/general.py index 46ac1615..6b025080 100644 --- a/RISE/figures/commonFuncs/plotGeneral.py +++ b/RISE/plotting/general.py @@ -4,7 +4,7 @@ import seaborn as sns from matplotlib.axes import Axes -from ...factorization import rise_pca_r2x +from ..factorization import rise_pca_r2x def plot_r2x(data, rank_vec, ax: Axes): diff --git a/RISE/figures/commonFuncs/plotPaCMAP.py b/RISE/plotting/pacmap.py similarity index 97% rename from RISE/figures/commonFuncs/plotPaCMAP.py rename to RISE/plotting/pacmap.py index 6b0dbdd2..bfb1244e 100644 --- a/RISE/figures/commonFuncs/plotPaCMAP.py +++ b/RISE/plotting/pacmap.py @@ -75,7 +75,7 @@ def plot_gene_pacmap(gene: str, X: anndata.AnnData, ax: Axes, clip_outliers=0.99 points = np.array(X.obsm["X_pf2_PaCMAP"]) canvas = _get_canvas(points) - data = pd.DataFrame(points, columns=("x", "y")) + data = pd.DataFrame(points, columns=["x", "y"]) # type: ignore values -= np.min(values) values /= np.max(values) @@ -126,7 +126,7 @@ def plot_wp_pacmap(X: anndata.AnnData, cmp: int, ax: Axes, cbarMax: float = 1.0) cmap = sns.diverging_palette(240, 10, as_cmap=True) canvas = _get_canvas(points) - data = pd.DataFrame(points, columns=("x", "y")) + data = pd.DataFrame(points, columns=["x", "y"]) # type: ignore values /= np.max(np.abs(values)) @@ -195,7 +195,7 @@ def plot_labels_pacmap( labels = labels.iloc[indices] canvas = _get_canvas(points) - data = pd.DataFrame(points, columns=("x", "y")) + data = pd.DataFrame(points, columns=["x", "y"]) # type: ignore data["label"] = pd.Categorical(labels) aggregation = canvas.points(data, "x", "y", agg=ds.count_cat("label")) diff --git a/RISE/figures/commonFuncs/seriate.py b/RISE/plotting/seriate.py similarity index 100% rename from RISE/figures/commonFuncs/seriate.py rename to RISE/plotting/seriate.py diff --git a/RISE/figures/figureS4.py b/RISE/plotting/stability.py similarity index 91% rename from RISE/figures/figureS4.py rename to RISE/plotting/stability.py index 90b0226c..1af88250 100644 --- a/RISE/figures/figureS4.py +++ b/RISE/plotting/stability.py @@ -1,5 +1,5 @@ """ -Figure S4 +Decomposition stability analysis and plotting functions. """ import anndata @@ -12,26 +12,9 @@ from tlviz.factor_tools import factor_match_score as fms from ..factorization import pf2 -from .common import getSetup, subplotLabel -# from ..imports import import_thomson - -def makeFigure(): - ax, f = getSetup((6, 3), (1, 2)) - subplotLabel(ax) - - # X = import_thomson() - # percentList = np.arange(0.0, 8.0, 5.0) - # plot_fms_percent_drop(X, ax[0], percentList=percentList, runs=3) - - # ranks = list(range(1, 3)) - # plot_fms_diff_ranks(X, ax[1], ranksList=ranks, runs=3) - - return f - - -def calculateFMS(A: anndata.AnnData, B: anndata.AnnData): +def calculateFMS(A: anndata.AnnData, B: anndata.AnnData) -> float: """Calculate Factor Match Score (FMS) between two RISE decompositions. Factor Match Score measures the similarity between two tensor decompositions @@ -80,7 +63,7 @@ def calculateFMS(A: anndata.AnnData, B: anndata.AnnData): ) ) - return fms(A_CP, B_CP, consider_weights=False, skip_mode=1) # type: ignore + return fms(A_CP, B_CP, consider_weights=False, skip_mode=1) def plot_fms_percent_drop( diff --git a/analysis/figures/commonFuncs/plotLupus.py b/analysis/figures/commonFuncs/plotLupus.py index e827c361..6a7e718d 100644 --- a/analysis/figures/commonFuncs/plotLupus.py +++ b/analysis/figures/commonFuncs/plotLupus.py @@ -10,7 +10,7 @@ predaccuracy_ranks_lupus, roc_lupus_fourtbatch, ) -from RISE.figures.commonFuncs.plotGeneral import cell_count_perc_lupus_df +from RISE.plotting import cell_count_perc_lupus_df def samples_only_lupus(X: anndata.AnnData): diff --git a/analysis/figures/figure2b_e.py b/analysis/figures/figure2b_e.py index 60d3aeb4..0a33f611 100644 --- a/analysis/figures/figure2b_e.py +++ b/analysis/figures/figure2b_e.py @@ -7,7 +7,7 @@ import pacmap from sklearn.decomposition import PCA -from RISE.figures.commonFuncs.plotPaCMAP import plot_labels_pacmap +from RISE.plotting import plot_labels_pacmap from .common import getSetup, subplotLabel diff --git a/analysis/figures/figure2f_h.py b/analysis/figures/figure2f_h.py index 9f1ac87d..40c6d583 100644 --- a/analysis/figures/figure2f_h.py +++ b/analysis/figures/figure2f_h.py @@ -6,7 +6,7 @@ import numpy as np import pandas as pd -from RISE.figures.commonFuncs.plotFactors import ( +from RISE.plotting import ( plot_condition_factors, plot_eigenstate_factors, plot_gene_factors, diff --git a/analysis/figures/figure3.py b/analysis/figures/figure3.py index 5669a1ee..80841853 100644 --- a/analysis/figures/figure3.py +++ b/analysis/figures/figure3.py @@ -8,18 +8,17 @@ import seaborn as sns from matplotlib.axes import Axes -from RISE.figures.commonFuncs.plotFactors import ( - plot_condition_factors, - plot_gene_factors, -) -from RISE.figures.commonFuncs.plotGeneral import ( +from RISE.plotting import ( cell_count_perc_df, gene_plot_cells, plot_avegene_per_category, plot_avegene_per_celltype, plot_cell_gene_corr, + plot_condition_factors, + plot_gene_factors, + plot_labels_pacmap, + plot_wp_pacmap, ) -from RISE.figures.commonFuncs.plotPaCMAP import plot_labels_pacmap, plot_wp_pacmap from .common import ( getSetup, diff --git a/analysis/figures/figure4d.py b/analysis/figures/figure4d.py index ec82b2b5..0fda359a 100644 --- a/analysis/figures/figure4d.py +++ b/analysis/figures/figure4d.py @@ -14,7 +14,7 @@ from analysis.figures.commonFuncs.plotLupus import samples_only_lupus from RISE.factorization import correct_conditions -from RISE.figures.commonFuncs.plotGeneral import rotate_xaxis, rotate_yaxis +from RISE.plotting import rotate_xaxis, rotate_yaxis from .common import getSetup, subplotLabel diff --git a/analysis/figures/figure4e_k.py b/analysis/figures/figure4e_k.py index c681b966..b0b54714 100644 --- a/analysis/figures/figure4e_k.py +++ b/analysis/figures/figure4e_k.py @@ -9,13 +9,13 @@ from matplotlib.axes import Axes from scipy.stats import pearsonr -from RISE.figures.commonFuncs.plotFactors import plot_gene_factors -from RISE.figures.commonFuncs.plotGeneral import ( +from RISE.plotting import ( avegene_per_status, cell_count_perc_lupus_df, + plot_gene_factors, + plot_wp_pacmap, rotate_xaxis, ) -from RISE.figures.commonFuncs.plotPaCMAP import plot_wp_pacmap from .common import getSetup, subplotLabel diff --git a/analysis/figures/figure5a_e.py b/analysis/figures/figure5a_e.py index f890b8a5..49f5f674 100644 --- a/analysis/figures/figure5a_e.py +++ b/analysis/figures/figure5a_e.py @@ -9,9 +9,13 @@ import seaborn as sns from matplotlib.axes import Axes -from RISE.figures.commonFuncs.plotFactors import plot_gene_factors -from RISE.figures.commonFuncs.plotGeneral import cell_count_perc_lupus_df, rotate_xaxis -from RISE.figures.commonFuncs.plotPaCMAP import plot_gene_pacmap, plot_wp_pacmap +from RISE.plotting import ( + cell_count_perc_lupus_df, + plot_gene_factors, + plot_gene_pacmap, + plot_wp_pacmap, + rotate_xaxis, +) from .common import getSetup, subplotLabel from .figure4e_k import plot_correlation_cmp_cell_count_perc diff --git a/analysis/figures/figure5f_j.py b/analysis/figures/figure5f_j.py index 0c335c5e..c798dbc2 100644 --- a/analysis/figures/figure5f_j.py +++ b/analysis/figures/figure5f_j.py @@ -8,7 +8,7 @@ import seaborn as sns from matplotlib.axes import Axes -from RISE.figures.commonFuncs.plotPaCMAP import plot_wp_pacmap +from RISE.plotting import plot_wp_pacmap from .common import getSetup, subplotLabel diff --git a/analysis/figures/figureS10.py b/analysis/figures/figureS10.py index ba61c055..8d621708 100644 --- a/analysis/figures/figureS10.py +++ b/analysis/figures/figureS10.py @@ -4,7 +4,7 @@ import anndata -from RISE.figures.commonFuncs.plotPaCMAP import plot_wp_pacmap +from RISE.plotting import plot_wp_pacmap from .common import getSetup, subplotLabel diff --git a/analysis/figures/figureS2.py b/analysis/figures/figureS2.py index bd17ba2a..76785a8d 100644 --- a/analysis/figures/figureS2.py +++ b/analysis/figures/figureS2.py @@ -10,8 +10,8 @@ import scib from sklearn.decomposition import PCA -# from .commonFuncs.plotGeneral import plot_r2x -from RISE.figures.commonFuncs.plotPaCMAP import plot_labels_pacmap +# from RISE.plotting import plot_r2x +from RISE.plotting import plot_labels_pacmap from .common import getSetup, subplotLabel diff --git a/analysis/figures/figureS3.py b/analysis/figures/figureS3.py index 25143806..35052fa1 100644 --- a/analysis/figures/figureS3.py +++ b/analysis/figures/figureS3.py @@ -6,7 +6,7 @@ import seaborn as sns from matplotlib.axes import Axes -from RISE.figures.commonFuncs.plotGeneral import cell_count_perc_df, rotate_xaxis +from RISE.plotting import cell_count_perc_df, rotate_xaxis from .common import getSetup, subplotLabel diff --git a/analysis/figures/figureS4.py b/analysis/figures/figureS4.py new file mode 100644 index 00000000..1004d2d5 --- /dev/null +++ b/analysis/figures/figureS4.py @@ -0,0 +1,19 @@ +""" +Figure S4 +""" + +from .common import getSetup, subplotLabel + + +def makeFigure(): + ax, f = getSetup((6, 3), (1, 2)) + subplotLabel(ax) + + # X = import_thomson() + # percentList = np.arange(0.0, 8.0, 5.0) + # plot_fms_percent_drop(X, ax[0], percentList=percentList, runs=3) + + # ranks = list(range(1, 3)) + # plot_fms_diff_ranks(X, ax[1], ranksList=ranks, runs=3) + + return f diff --git a/analysis/figures/figureS5.py b/analysis/figures/figureS5.py index dd36f834..dcc4356e 100644 --- a/analysis/figures/figureS5.py +++ b/analysis/figures/figureS5.py @@ -5,7 +5,7 @@ import anndata import seaborn as sns -from RISE.figures.commonFuncs.plotGeneral import cell_count_perc_df, rotate_xaxis +from RISE.plotting import cell_count_perc_df, rotate_xaxis from .common import getSetup, subplotLabel diff --git a/analysis/figures/figureS6.py b/analysis/figures/figureS6.py index e14f1c77..c1d75872 100644 --- a/analysis/figures/figureS6.py +++ b/analysis/figures/figureS6.py @@ -4,7 +4,7 @@ import anndata -from RISE.figures.commonFuncs.plotPaCMAP import plot_labels_pacmap, plot_wp_pacmap +from RISE.plotting import plot_labels_pacmap, plot_wp_pacmap from .common import getSetup, subplotLabel diff --git a/analysis/figures/figureS8g_h.py b/analysis/figures/figureS8g_h.py index 93d45a1b..ab46e8d8 100644 --- a/analysis/figures/figureS8g_h.py +++ b/analysis/figures/figureS8g_h.py @@ -6,12 +6,12 @@ from analysis.figures.commonFuncs.plotLupus import samples_only_lupus from RISE.factorization import correct_conditions -from RISE.figures.commonFuncs.plotFactors import ( +from RISE.plotting import ( plot_condition_factors, plot_eigenstate_factors, plot_gene_factors, + plot_labels_pacmap, ) -from RISE.figures.commonFuncs.plotPaCMAP import plot_labels_pacmap from .common import getSetup, subplotLabel diff --git a/analysis/figures/figureS9a_d.py b/analysis/figures/figureS9a_d.py index dcac8f8d..cbeab52d 100644 --- a/analysis/figures/figureS9a_d.py +++ b/analysis/figures/figureS9a_d.py @@ -21,7 +21,8 @@ from analysis.imports import import_lupus from RISE.factorization import pf2 -from RISE.figures.common import getSetup, subplotLabel + +from .common import getSetup, subplotLabel # Simplified to single-line comments for configuration flags RECOMPUTE = False diff --git a/analysis/figures/figureS9e_f.py b/analysis/figures/figureS9e_f.py index 68243ae4..d17ccb36 100644 --- a/analysis/figures/figureS9e_f.py +++ b/analysis/figures/figureS9e_f.py @@ -11,7 +11,7 @@ from analysis.figures.commonFuncs.plotLupus import samples_only_lupus from analysis.logisticReg import logistic_regression from RISE.factorization import correct_conditions -from RISE.figures.commonFuncs.plotGeneral import cell_count_perc_lupus_df, rotate_xaxis +from RISE.plotting import cell_count_perc_lupus_df, rotate_xaxis from .common import getSetup, subplotLabel diff --git a/docs/api.rst b/docs/api.rst index aff2a400..8fbe6b0b 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -60,7 +60,7 @@ General Plotting ~~~~~~~~~~~~~~~~ .. py:function:: plot_r2x(data: anndata.AnnData, rank_vec, ax: matplotlib.axes.Axes) - :module: RISE.figures.commonFuncs.plotGeneral + :module: RISE.plotting Plot variance explained (R²X) for RISE and PCA across different ranks. @@ -79,7 +79,7 @@ Factor Plotting ~~~~~~~~~~~~~~~ .. py:function:: plot_condition_factors(data: anndata.AnnData, ax: matplotlib.axes.Axes, cond: str = 'Condition', log_transform: bool = True, cond_group_labels: pandas.Series = None, ThomsonNorm=False, color_key=None, group_cond=False) - :module: RISE.figures.commonFuncs.plotFactors + :module: RISE.plotting Plot condition factors as a heatmap showing how conditions contribute to components. @@ -103,7 +103,7 @@ Factor Plotting :type group_cond: bool, optional .. py:function:: plot_eigenstate_factors(data: anndata.AnnData, ax: matplotlib.axes.Axes) - :module: RISE.figures.commonFuncs.plotFactors + :module: RISE.plotting Plot eigen-state factors as a heatmap showing cell state patterns. @@ -115,7 +115,7 @@ Factor Plotting :type ax: matplotlib.axes.Axes .. py:function:: plot_gene_factors(data: anndata.AnnData, ax: matplotlib.axes.Axes, weight=0.08, trim=True) - :module: RISE.figures.commonFuncs.plotFactors + :module: RISE.plotting Plot gene factors as a heatmap showing which genes contribute to each component. @@ -134,7 +134,7 @@ PaCMAP Visualization ~~~~~~~~~~~~~~~~~~~~ .. py:function:: plot_labels_pacmap(X: anndata.AnnData, labelType: str, ax: matplotlib.axes.Axes, condition=None, cmap: str = 'tab20', color_key=None) - :module: RISE.figures.commonFuncs.plotPaCMAP + :module: RISE.plotting Plot PaCMAP embedding colored by categorical labels (cell type or condition). @@ -154,7 +154,7 @@ PaCMAP Visualization :type color_key: list, optional .. py:function:: plot_gene_pacmap(gene: str, X: anndata.AnnData, ax: matplotlib.axes.Axes, clip_outliers=0.9995) - :module: RISE.figures.commonFuncs.plotPaCMAP + :module: RISE.plotting Plot PaCMAP embedding colored by gene expression levels. @@ -170,7 +170,7 @@ PaCMAP Visualization :type clip_outliers: float, optional .. py:function:: plot_wp_pacmap(X: anndata.AnnData, cmp: int, ax: matplotlib.axes.Axes, cbarMax: float = 1.0) - :module: RISE.figures.commonFuncs.plotPaCMAP + :module: RISE.plotting Plot PaCMAP embedding colored by weighted projections for a component. @@ -189,7 +189,7 @@ Factor Stability ~~~~~~~~~~~~~~~~ .. py:function:: plot_fms_diff_ranks(X: anndata.AnnData, ax: matplotlib.axes.Axes, ranksList: list[int], runs: int) - :module: RISE.figures.figureS4 + :module: RISE.plotting Plot Factor Match Score (FMS) across different ranks to assess stability. diff --git a/docs/generate_tutorial_figures.py b/docs/generate_tutorial_figures.py index d10a6767..9b1300bb 100644 --- a/docs/generate_tutorial_figures.py +++ b/docs/generate_tutorial_figures.py @@ -14,18 +14,16 @@ # Import RISE modules from analysis.imports import import_thomson from RISE.factorization import pf2 -from RISE.figures.commonFuncs.plotFactors import ( +from RISE.plotting import ( plot_condition_factors, plot_eigenstate_factors, + plot_fms_diff_ranks, plot_gene_factors, -) -from RISE.figures.commonFuncs.plotGeneral import plot_r2x -from RISE.figures.commonFuncs.plotPaCMAP import ( plot_gene_pacmap, plot_labels_pacmap, + plot_r2x, plot_wp_pacmap, ) -from RISE.figures.figureS4 import plot_fms_diff_ranks print("Loading dataset...") X = import_thomson() diff --git a/docs/tutorial.rst b/docs/tutorial.rst index dcdcc5ae..cac28a12 100644 --- a/docs/tutorial.rst +++ b/docs/tutorial.rst @@ -53,7 +53,7 @@ Determine the optimal component/rank by plotting the variance explained (R²X) a .. code-block:: python - from RISE.figures.commonFuncs.plotGeneral import plot_r2x + from RISE.plotting import plot_r2x import matplotlib.pyplot as plt ranks = [1, 5, 10, 15, 20, 25, 30] @@ -73,7 +73,7 @@ Measure the reproducibility of the RISE factorization across different ranks. An .. code-block:: python - from RISE.figures.figureS4 import plot_fms_diff_ranks + from RISE.plotting import plot_fms_diff_ranks fig, ax = plt.subplots(figsize=(5, 5)) rank_list = list(ranks) @@ -125,11 +125,11 @@ Visualizing the Factors **Visualize Condition Factors** Examine how each experimental condition contributes to the identified patterns. Log-transforming these factors allows for easier interpretation of condition-specific effects. -Several plotting functions are available in the ``RISE.figures.commonFuncs.plotFactors`` and ``RISE.figures.commonFuncs.plotPaCMAP`` modules. +Several plotting functions are available in the ``RISE.plotting`` package. .. code-block:: python - from RISE.figures.commonFuncs.plotFactors import plot_condition_factors + from RISE.plotting import plot_condition_factors fig, ax = plt.subplots(figsize=(8, 8)) @@ -149,7 +149,7 @@ Explore the latent space of cells using nonlinear dimensionality reduction metho .. code-block:: python - from RISE.figures.commonFuncs.plotPaCMAP import plot_labels_pacmap + from RISE.plotting import plot_labels_pacmap fig, ax = plt.subplots(figsize=(8, 8)) @@ -167,7 +167,7 @@ Analyze how each cell state contributes to the identified patterns. Each eigen-s .. code-block:: python - from RISE.figures.commonFuncs.plotFactors import plot_eigenstate_factors + from RISE.plotting import plot_eigenstate_factors fig, ax = plt.subplots(figsize=(4, 4)) @@ -188,7 +188,7 @@ Identify which genes are highly weighted in each component, revealing coordinate .. code-block:: python - from RISE.figures.commonFuncs.plotFactors import plot_gene_factors + from RISE.plotting import plot_gene_factors fig, ax = plt.subplots(figsize=(7, 8)) @@ -211,7 +211,7 @@ Overlay specific gene expression on the cell embedding to see which cells expres .. code-block:: python - from RISE.figures.commonFuncs.plotPaCMAP import plot_gene_pacmap + from RISE.plotting import plot_gene_pacmap fig, ax = plt.subplots(figsize=(8, 8)) @@ -232,7 +232,7 @@ Visualize how cells contribute to specific components using weighted projections .. code-block:: python - from RISE.figures.commonFuncs.plotPaCMAP import plot_wp_pacmap + from RISE.plotting import plot_wp_pacmap fig, ax = plt.subplots(figsize=(8, 8)) diff --git a/makefile b/makefile index ce4b7e18..c950ac84 100644 --- a/makefile +++ b/makefile @@ -18,7 +18,9 @@ test: .venv coverage.xml: .venv uv run pytest --junitxml=junit.xml --cov=RISE --cov-report xml:coverage.xml -ty: .venv +lint: .venv + uv run ruff format . + uv run ruff check . --fix uv run ty check RISE analysis clean: From a3b8d117caf6ab7bf36c66eb06e6147da41503ce Mon Sep 17 00:00:00 2001 From: Aaron Meyer Date: Sun, 21 Jun 2026 07:45:07 -0700 Subject: [PATCH 4/8] Fixed ruff checks --- RISE/factorization.py | 6 +++-- RISE/plotting/factors.py | 9 ++++--- RISE/plotting/seriate.py | 39 +++++++++++++++++-------------- analysis/__init__.py | 4 +++- docs/generate_tutorial_figures.py | 9 +++---- 5 files changed, 40 insertions(+), 27 deletions(-) diff --git a/RISE/factorization.py b/RISE/factorization.py index ce745a10..bc224a2e 100644 --- a/RISE/factorization.py +++ b/RISE/factorization.py @@ -95,8 +95,10 @@ def pf2( - X.uns["Pf2_B"]: Eigen-state factors (shape: rank, rank) - X.varm["Pf2_C"]: Gene factors (shape: n_genes, rank) - X.obsm["projections"]: Cell projections (shape: n_cells, rank) - - X.obsm["weighted_projections"]: Weighted cell projections (shape: n_cells, rank) - - X.obsm["X_pf2_PaCMAP"]: PaCMAP embedding (shape: n_cells, 2) if doEmbedding=True + - X.obsm["weighted_projections"]: Weighted cell projections + (shape: n_cells, rank) + - X.obsm["X_pf2_PaCMAP"]: PaCMAP embedding (shape: n_cells, 2) + if doEmbedding=True """ pf_out, _ = parafac2_nd( X, rank=rank, random_state=random_state, tol=tolerance, n_iter_max=max_iter diff --git a/RISE/plotting/factors.py b/RISE/plotting/factors.py index b9a99c89..6a30ed18 100644 --- a/RISE/plotting/factors.py +++ b/RISE/plotting/factors.py @@ -22,7 +22,8 @@ def plot_condition_factors( color_key=None, group_cond=False, ): - """Plot condition factors as a heatmap showing how conditions contribute to components. + """Plot condition factors as a heatmap showing how conditions contribute to + components. This visualization shows how each experimental condition (rows) contributes to each RISE component (columns). High values indicate strong association between @@ -46,7 +47,8 @@ def plot_condition_factors( Series mapping conditions to group labels for colored row annotations. Useful for grouping related conditions (e.g., drug classes, patient cohorts). ThomsonNorm : bool, optional (default: False) - If True, normalizes factors using only control conditions (those containing 'CTRL'). + If True, normalizes factors using only control conditions (those + containing 'CTRL'). color_key : list, optional (default: None) Custom colors for condition group labels. If None, uses default palette. group_cond : bool, optional (default: False) @@ -162,7 +164,8 @@ def plot_gene_factors(data: anndata.AnnData, ax: Axes, weight=0.08, trim=True): This visualization reveals coordinated gene modules by showing which genes (rows) are highly weighted in each component (columns). The weight parameter filters out - genes with low contributions, focusing on the most important genes for interpretation. + genes with low contributions, focusing on the most important genes for + interpretation. Parameters ---------- diff --git a/RISE/plotting/seriate.py b/RISE/plotting/seriate.py index 9917019a..5b9b4f3e 100644 --- a/RISE/plotting/seriate.py +++ b/RISE/plotting/seriate.py @@ -41,20 +41,22 @@ def seriate( dists: numpy.ndarray, approximation_multiplier: int = 1000, timeout: float = 2.0 ) -> list[int]: """ - Order the elements of a set so that the sum of sequential pairwise distances is minimal. + Order the elements of a set so that the sum of sequential pairwise + distances is minimal. We solve the Travelling Salesman Problem (TSP) under the hood. Reference: http://nicolas.kruchten.com/content/2018/02/seriation/ - :param dists: Either a condensed pdist-like or a symmetric square distance matrix. - :param approximation_multiplier: Multiply by this number before converting distances \ - to integers. - :param timeout: Maximum amount of time allowed to spend for solving the TSP, in seconds. \ - This value cannot be less than 0. If timeout is 0 it will try to solve \ - the problem with timeout = 1, and double the timeout every time it fails \ - until a valid solution is found. - :return: list with ordered element indexes, the same length as the number of elements \ - involved in calculating `dists`. + :param dists: Either a condensed pdist-like or a symmetric square distance + matrix. + :param approximation_multiplier: Multiply by this number before converting + distances to integers. + :param timeout: Maximum amount of time allowed to spend for solving the TSP, + in seconds. This value cannot be less than 0. If timeout is 0 + it will try to solve the problem with timeout = 1, and double + the timeout every time it fails until a valid solution is found. + :return: list with ordered element indexes, the same length as the number of + elements involved in calculating `dists`. """ _validate_data(dists) if timeout > 0: @@ -83,17 +85,20 @@ def _seriate( dists: numpy.ndarray, approximation_multiplier=1000, timeout=2.0 ) -> list[int]: """ - Order the elements of a set so that the sum of sequential pairwise distances is minimal. + Order the elements of a set so that the sum of sequential pairwise + distances is minimal. We solve the Travelling Salesman Problem (TSP) under the hood. Reference: http://nicolas.kruchten.com/content/2018/02/seriation/ - :param dists: Either a condensed pdist-like or a symmetric square distance matrix. - :param approximation_multiplier: Multiply by this number before converting distances \ - to integers. - :param timeout: Maximum amount of time allowed to spend for solving the TSP, in seconds. - :return: list with ordered element indexes, the same length as the number of elements \ - involved in calculating `dists`. + :param dists: Either a condensed pdist-like or a symmetric square distance + matrix. + :param approximation_multiplier: Multiply by this number before converting + distances to integers. + :param timeout: Maximum amount of time allowed to spend for solving the TSP, + in seconds. + :return: list with ordered element indexes, the same length as the number of + elements involved in calculating `dists`. """ assert dists[dists < 0].size == 0, "distances must be non-negative" assert timeout > 0 diff --git a/analysis/__init__.py b/analysis/__init__.py index cd0d3b9c..7736a538 100644 --- a/analysis/__init__.py +++ b/analysis/__init__.py @@ -1 +1,3 @@ -"""Analysis package containing paper-specific datasets, gating, regression, and figure-generation scripts.""" +"""Analysis package containing paper-specific datasets, gating, regression, +and figure-generation scripts. +""" diff --git a/docs/generate_tutorial_figures.py b/docs/generate_tutorial_figures.py index 9b1300bb..c3505517 100644 --- a/docs/generate_tutorial_figures.py +++ b/docs/generate_tutorial_figures.py @@ -7,12 +7,9 @@ import matplotlib.pyplot as plt -# Create output directory -output_dir = Path(__file__).parent / "_static" / "tutorial_images" -output_dir.mkdir(parents=True, exist_ok=True) +from analysis.imports import import_thomson # Import RISE modules -from analysis.imports import import_thomson from RISE.factorization import pf2 from RISE.plotting import ( plot_condition_factors, @@ -25,6 +22,10 @@ plot_wp_pacmap, ) +# Create output directory +output_dir = Path(__file__).parent / "_static" / "tutorial_images" +output_dir.mkdir(parents=True, exist_ok=True) + print("Loading dataset...") X = import_thomson() From 99fbae2c905865f628a4837c0e0978b29f67a742 Mon Sep 17 00:00:00 2001 From: Aaron Meyer Date: Sun, 21 Jun 2026 07:49:00 -0700 Subject: [PATCH 5/8] Last fix --- analysis/notebooks/thomson/Thomson_Annot.ipynb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/analysis/notebooks/thomson/Thomson_Annot.ipynb b/analysis/notebooks/thomson/Thomson_Annot.ipynb index 9c4ef4a3..a5d1ef82 100644 --- a/analysis/notebooks/thomson/Thomson_Annot.ipynb +++ b/analysis/notebooks/thomson/Thomson_Annot.ipynb @@ -451,7 +451,6 @@ } ], "source": [ - "{\"B Cells\", \"Monocytes\", \"DCs\", \"NK Cells\", \"T Cells\"}\n", "\n", "celltypedict_layer1 = {\n", " \"0\": \"Monocytes\",\n", @@ -574,7 +573,7 @@ " \"Follicular T\": [\"ICOS\", \"PDCD1\", \"BCL6\", \"CXCR5\", \"CD200\", \"P2RX7\", \"CD3D\"],\n", " \"Helper T\": [\"CCR4\", \"CD4\", \"IL13\", \"CD28\", \"CD3G\", \"IL2\", \"CCR6\"],\n", " \"Memory T\": [\"CCR7\", \"CD2\", \"PTPRC\", \"CD28\", \"LEF1\", \"S100A8\", \"GIMAP4\"],\n", - " \"Follicular T\": [\n", + " \"Treg\": [\n", " \"IKZF2\",\n", " \"FOXP3\",\n", " \"CCR4\",\n", From fdf04391a6db8f4a874180a862278dcad1d074cb Mon Sep 17 00:00:00 2001 From: Aaron Meyer Date: Sun, 21 Jun 2026 08:05:51 -0700 Subject: [PATCH 6/8] Fix warnings --- RISE/factorization.py | 4 ++-- analysis/gating.py | 2 +- analysis/imports.py | 10 +++++----- pyproject.toml | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/RISE/factorization.py b/RISE/factorization.py index bc224a2e..02271e69 100644 --- a/RISE/factorization.py +++ b/RISE/factorization.py @@ -6,7 +6,6 @@ from scipy.stats import gmean from sklearn.decomposition import PCA from sklearn.linear_model import LinearRegression -from sklearn.preprocessing import scale from tqdm import tqdm @@ -147,7 +146,8 @@ def rise_pca_r2x(X: anndata.AnnData, ranks): r2x_rise[index] = R2X # Mean center because this is done within RISE - XX = scale(XX.todense(), with_mean=True, with_std=False) + XX = XX.toarray() + XX = XX - np.mean(XX, axis=0) pca = PCA(n_components=ranks[-1]) pca.fit(XX) diff --git a/analysis/gating.py b/analysis/gating.py index eb2c2cd1..eba46bf9 100644 --- a/analysis/gating.py +++ b/analysis/gating.py @@ -19,7 +19,7 @@ def gateThomsonCells(X) -> npt.ArrayLike: """Manually gates cell types for Thomson PaCMAP""" cellTypeDF = pd.read_csv("analysis/data/Thomson/ThomsonCellTypes.csv", index_col=0) cellTypeDF.index.name = "cell_barcode" - X.obs = X.obs.join(cellTypeDF, on="cell_barcode", how="inner") + X.obs = X.obs.join(cellTypeDF, how="inner") X.obs["Cell Type"] = X.obs["Cell Type"].values.astype(str) X.obs["Cell Type2"] = X.obs["Cell Type2"].values.astype(str) diff --git a/analysis/imports.py b/analysis/imports.py index c01a5c6b..91a05e76 100644 --- a/analysis/imports.py +++ b/analysis/imports.py @@ -21,25 +21,25 @@ def import_thomson() -> anndata.AnnData: X.obs = pd.DataFrame( { - "cell_barcode": metafile["cell_barcode"], "Condition": pd.Categorical(metafile["sample_id"]), - } + }, + index=metafile["cell_barcode"] ) + X.obs.index.name = "cell_barcode" doubletDF = pd.read_csv("analysis/data/Thomson/ThomsonDoublets.csv", index_col=0) doubletDF.index.name = "cell_barcode" - X.obs = X.obs.join(doubletDF, on="cell_barcode", how="inner") + X.obs = X.obs.join(doubletDF, how="inner") singlet_indices = X.obs.loc[X.obs["doublet"] == 0].index.values - X.obs = X.obs.reset_index(drop=True) X = X[singlet_indices, :] - X.obs = X.obs.set_index("cell_barcode") gateThomsonCells(X) return prepare_dataset(X, "Condition", geneThreshold=0.01) + def import_lupus(geneThreshold: float = 0.1) -> anndata.AnnData: """Import Lupus PBMC dataset. diff --git a/pyproject.toml b/pyproject.toml index cf718297..45a5a10d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "RISE" -version = "0.1.0" +version = "1.1.0" description = "Single cell analysis across conditions using PARAFAC2." authors = [{name = "Andrew Ramirez"}, {name = "Aaron Meyer", email = "git@asmlab.org" }] license = "MIT" From 89d75746c8dce280567e5328f0cc44c32027af5f Mon Sep 17 00:00:00 2001 From: Aaron Meyer Date: Sun, 28 Jun 2026 11:42:05 -0700 Subject: [PATCH 7/8] Lupus is now compressed --- analysis/imports.py | 14 ++++- .../notebooks/thomson/Thomson_Annot.ipynb | 1 - analysis/tests/test_import.py | 4 +- pyproject.toml | 1 + uv.lock | 62 ++++++++++++------- 5 files changed, 54 insertions(+), 28 deletions(-) diff --git a/analysis/imports.py b/analysis/imports.py index 91a05e76..88872e9b 100644 --- a/analysis/imports.py +++ b/analysis/imports.py @@ -3,6 +3,8 @@ import scanpy as sc from parafac2.normalize import prepare_dataset +import hdf5plugin + from .gating import gateThomsonCells @@ -23,7 +25,7 @@ def import_thomson() -> anndata.AnnData: { "Condition": pd.Categorical(metafile["sample_id"]), }, - index=metafile["cell_barcode"] + index=metafile["cell_barcode"], ) X.obs.index.name = "cell_barcode" @@ -39,7 +41,6 @@ def import_thomson() -> anndata.AnnData: return prepare_dataset(X, "Condition", geneThreshold=0.01) - def import_lupus(geneThreshold: float = 0.1) -> anndata.AnnData: """Import Lupus PBMC dataset. @@ -59,7 +60,14 @@ def import_lupus(geneThreshold: float = 0.1) -> anndata.AnnData: 'SLE_status': SLE status: healthy or SLE} """ - X = anndata.read_h5ad("/opt/andrew/lupus/raw_lupus.h5ad", backed="r") + X = anndata.read_h5ad("/opt/andrew/lupus/lupus.h5ad", backed="r") + + # Replace X with raw.X in memory using the raw backing + X = anndata.AnnData( + X=X.raw.X, + obs=X.obs, + var=X.raw.var, + ) protein = anndata.read_h5ad("/opt/andrew/lupus/Lupus_study_protein_adjusted.h5ad") protein_df = protein.to_df() diff --git a/analysis/notebooks/thomson/Thomson_Annot.ipynb b/analysis/notebooks/thomson/Thomson_Annot.ipynb index a5d1ef82..c072921f 100644 --- a/analysis/notebooks/thomson/Thomson_Annot.ipynb +++ b/analysis/notebooks/thomson/Thomson_Annot.ipynb @@ -451,7 +451,6 @@ } ], "source": [ - "\n", "celltypedict_layer1 = {\n", " \"0\": 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changed, 133 insertions(+), 127 deletions(-) diff --git a/analysis/imports.py b/analysis/imports.py index 88872e9b..849c1902 100644 --- a/analysis/imports.py +++ b/analysis/imports.py @@ -1,15 +1,17 @@ +import h5py import anndata import pandas as pd import scanpy as sc +from anndata.io import read_elem from parafac2.normalize import prepare_dataset import hdf5plugin -from .gating import gateThomsonCells - def import_thomson() -> anndata.AnnData: """Import Thompson lab PBMC dataset.""" + from .gating import gateThomsonCells + # Cell barcodes, sample id of treatment and sample number metafile = pd.read_csv("analysis/data/Thomson/meta.csv", usecols=[0, 1]) X = sc.read_10x_mtx( @@ -60,14 +62,15 @@ def import_lupus(geneThreshold: float = 0.1) -> anndata.AnnData: 'SLE_status': SLE status: healthy or SLE} """ - X = anndata.read_h5ad("/opt/andrew/lupus/lupus.h5ad", backed="r") + # Read only obs, raw/X, and raw/var — the dense processed X slot (9.6 GB float32) + # causes hdf5plugin to allocate ~180 GB of decompression buffers when the file is + # opened, even in backed mode. h5py lets us skip it entirely. + with h5py.File("/opt/andrew/lupus/lupus.h5ad", "r") as f: + obs = read_elem(f["obs"]) + raw_var = read_elem(f["raw/var"]) + raw_X = read_elem(f["raw/X"]) - # Replace X with raw.X in memory using the raw backing - X = anndata.AnnData( - X=X.raw.X, - obs=X.obs, - var=X.raw.var, - ) + X = anndata.AnnData(X=raw_X, obs=obs, var=raw_var) protein = anndata.read_h5ad("/opt/andrew/lupus/Lupus_study_protein_adjusted.h5ad") protein_df = protein.to_df() @@ -90,6 +93,9 @@ def import_lupus(geneThreshold: float = 0.1) -> anndata.AnnData: X.obs = X.obs.merge(protein_df, how="left", left_index=True, right_index=True) # Get rid of IGTB1906_IGTB1906:dmx_count_AHCM2CDMXX_YE_0831 (Only 3 cells) - X = X[X.obs["Condition"] != "IGTB1906_IGTB1906:dmx_count_AHCM2CDMXX_YE_0831"] - - return prepare_dataset(X, "Condition", geneThreshold=geneThreshold) + # .copy() materialises the boolean-mask view before prepare_dataset; without it, + # prepare_dataset's `X.X = csr_array(X.X)` triggers a sparse setitem on the parent + # matrix (parent._X[bool_array, :] = value) which forces scipy to convert the + # 1.26M×32738 CSR to LIL/dense → OOM. + mask = X.obs["Condition"] != "IGTB1906_IGTB1906:dmx_count_AHCM2CDMXX_YE_0831" + return prepare_dataset(X[mask].copy(), "Condition", geneThreshold=geneThreshold) diff --git a/pyproject.toml b/pyproject.toml index 46fc4942..f8964ecd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ dependencies = [ "scikit-learn>=1.6", "pandas>=2.2.1", "tensorly>=0.8.1", - "parafac2 @ git+https://github.com/meyer-lab/parafac2.git@v1.2.0", + "parafac2 @ git+https://github.com/meyer-lab/parafac2.git@v1.2.2", "anndata>=0.10.3", "pacmap>=0.7.1", "tqdm>=4.66.1", diff --git a/uv.lock b/uv.lock index b2026c7a..3cdfdaea 100644 --- a/uv.lock +++ b/uv.lock @@ -21,7 +21,7 @@ wheels = [ [[package]] name = "anndata" -version = "0.12.17" +version = "0.12.18" 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