[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.1
+    rev: v0.4.3.9026
     hooks:
       - id: style-files
         args: [--style_pkg=styler, --style_fun=tidyverse_style]
@@ -13,7 +13,7 @@ repos:
       - id: deps-in-desc
         args: [--allow_private_imports]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v6.0.0
     hooks:
       - id: end-of-file-fixer
         exclude: '\.Rd'

R/DOT.R

@@ -11,7 +11,6 @@ build_model_dot <- function() {
 }
 
 
-
 #' Deconvolute with DOT
 #'
 #' Runs DOT deconvolution and returns the DOT weight matrix with column names

R/benchmarking.R

@@ -123,9 +123,6 @@ plot_scatter <- function(spe = NULL, value1, value2, spe1 = NULL, spe2 = NULL, l
 }
 
 
-
-
-
 #' Compare Signatures
 #'
 #' Creates a scatterplot comparing two signature matrices across shared genes.

R/cluster.R

@@ -59,7 +59,6 @@ cluster <- function(spe,
     cli::cli_alert_info(paste("Cluster resolution:", toString(clusres)))
 
 
-
     cli::cli_progress_step("Extracting data", msg_done = "Extracted data for clustering")
 
     # create seurat object
@@ -139,7 +138,6 @@ cluster <- function(spe,
   }
 
 
-
   cli::cli_progress_done()
 
   return(spe)
@@ -199,7 +197,6 @@ get_cluster_features <- function(spe,
   clusters <- colData(spe)[, clusterid]
 
 
-
   # Scores
   if (spmethod == "expression") {
     if (is.element("cpm", assayNames(spe)) && !is.null(spe@assays@data$cpm)) {

R/deconvolution_algorithms.R

@@ -228,8 +228,6 @@ deconvolute <- function(spatial_obj, signature = NULL, single_cell_obj = NULL,
   cli::cli_progress_step("testing parameter", msg_done = "parameter OK")
 
 
-
-
   if (is.null(spatial_obj)) {
     stop("Parameter 'spatial_obj' is missing or null, but is required.")
   }

R/preprocess.R

@@ -110,7 +110,6 @@ preprocess <- function(object, min_umi = 500, max_umi = NULL, assay = "counts",
   }
 
 
-
   cli::cli_progress_step(
     msg = "Checking for ENSEMBL Identifiers",
     msg_done = "Finished Preprocessing"

R/spatial_correlation.R

@@ -102,7 +102,6 @@ spatialcorr <- function(spe,
   }
 
 
-
   # Select variables of interests
   # If variables is not provided but method is specified, the function selects variables based on those available in the dataset that start with the specified method.
   if (is.null(variables) && !is.null(method)) {

R/subset.R

@@ -117,10 +117,6 @@ subsetSCE <- function(sce, cell_type_col = "celltype_major", scenario = "even",
 }
 
 
-
-
-
-
 #' Subset a SpatialExperiment by Spatial Coordinates
 #'
 #' Filters a `SpatialExperiment` to spots that fall within the provided x/y ranges

R/utils.R

@@ -287,7 +287,6 @@ checkENSEMBL <- function(names) {
 }
 
 
-
 #' Annotate Specific Spots in a SpatialExperiment
 #'
 #' Adds a new `colData` column that marks selected spots with `value_pos` and all

R/visualization.R

@@ -491,7 +491,6 @@ plot_comparison <- function(spe, cell_type_1 = NULL, cell_type_2 = NULL,
 }
 
 
-
 #' Plot Gene Expression
 #'
 #' Generate a spatial hex plot for a single gene from a `SpatialExperiment`.
@@ -736,8 +735,6 @@ make_baseplot <- function(spe, df, to_plot, palette = "Mako", transform_scale =
   }
 
 
-
-
   # Check if plot is smoothed
   if (smooth) {
     smooth_suffix <- "smoothed"

docs/deps/clipboard.js-2.0.11/clipboard.min.js

@@ -373,7 +373,7 @@
             e.oMatchesSelector ||
             e.webkitMatchesSelector),
           (t.exports = function (t, e) {
-            for (; t && 9 !== t.nodeType; ) {
+            for (; t && 9 !== t.nodeType;) {
               if ("function" == typeof t.matches && t.matches(e)) return t;
               t = t.parentNode;
             }

docs/deps/jquery-3.6.0/jquery-3.6.0.js

@@ -2408,15 +2408,15 @@
                 : argument > length
                   ? length
                   : argument;
-            for (; --i >= 0; ) {
+            for (; --i >= 0;) {
               matchIndexes.push(i);
             }
             return matchIndexes;
           }),
 
           gt: createPositionalPseudo(function (matchIndexes, length, argument) {
             var i = argument < 0 ? argument + length : argument;
-            for (; ++i < length; ) {
+            for (; ++i < length;) {
               matchIndexes.push(i);
             }
             return matchIndexes;
@@ -8099,7 +8099,7 @@
           }
         }
 
-        for (index = timers.length; index--; ) {
+        for (index = timers.length; index--;) {
           if (
             timers[index].elem === this &&
             (type == null || timers[index].queue === type)
@@ -8141,7 +8141,7 @@
         }
 
         // Look for any active animations, and finish them
-        for (index = timers.length; index--; ) {
+        for (index = timers.length; index--;) {
           if (timers[index].elem === this && timers[index].queue === type) {
             timers[index].anim.stop(true);
             timers.splice(index, 1);

docs/deps/jquery-3.6.0/jquery-3.6.0.min.js

@@ -1202,11 +1202,11 @@
             return e;
           }),
           lt: ve(function (e, t, n) {
-            for (var r = n < 0 ? n + t : t < n ? t : n; 0 <= --r; ) e.push(r);
+            for (var r = n < 0 ? n + t : t < n ? t : n; 0 <= --r;) e.push(r);
             return e;
           }),
           gt: ve(function (e, t, n) {
-            for (var r = n < 0 ? n + t : n; ++r < t; ) e.push(r);
+            for (var r = n < 0 ? n + t : n; ++r < t;) e.push(r);
             return e;
           }),
         },
@@ -3123,13 +3123,11 @@
         l,
         c = e.cloneNode(!0),
         f = ie(e);
-      if (
-        !(
-          y.noCloneChecked ||
-          (1 !== e.nodeType && 11 !== e.nodeType) ||
-          S.isXMLDoc(e)
-        )
-      )
+      if (!(
+        y.noCloneChecked ||
+        (1 !== e.nodeType && 11 !== e.nodeType) ||
+        S.isXMLDoc(e)
+      ))
         for (a = ve(c), r = 0, i = (o = ve(e)).length; r < i; r++)
           ((s = o[r]),
             (u = a[r]),
@@ -4031,7 +4029,7 @@
               r = Y.get(this);
             if (t) r[t] && r[t].stop && a(r[t]);
             else for (t in r) r[t] && r[t].stop && it.test(t) && a(r[t]);
-            for (t = n.length; t--; )
+            for (t = n.length; t--;)
               n[t].elem !== this ||
                 (null != i && n[t].queue !== i) ||
                 (n[t].anim.stop(o), (e = !1), n.splice(t, 1));

docs/deps/search-1.0.0/autocomplete.jquery.min.js

@@ -918,7 +918,7 @@
     function g(a) {
       var b;
       if (!this._callbacks) return this;
-      for (a = a.split(l); (b = a.shift()); ) delete this._callbacks[b];
+      for (a = a.split(l); (b = a.shift());) delete this._callbacks[b];
       return this;
     }
     function h(a) {
@@ -962,8 +962,8 @@
     function e() {
       if (!h) {
         ((n = !1), (h = !0));
-        for (var a = m.length, b = setTimeout(d); a; ) {
-          for (i = m, m = []; i && ++l < a; ) i[l].run();
+        for (var a = m.length, b = setTimeout(d); a;) {
+          for (i = m, m = []; i && ++l < a;) i[l].run();
           ((l = -1), (a = m.length));
         }
         ((i = null), (l = -1), (h = !1), clearTimeout(b));
@@ -1069,8 +1069,8 @@
       if (!p) {
         var a = e(g);
         p = !0;
-        for (var b = o.length; b; ) {
-          for (n = o, o = []; ++q < b; ) n && n[q].run();
+        for (var b = o.length; b;) {
+          for (n = o, o = []; ++q < b;) n && n[q].run();
           ((q = -1), (b = o.length));
         }
         ((n = null), (p = !1), f(a));

docs/deps/search-1.0.0/fuse.min.js

@@ -626,7 +626,7 @@ var e, t;
               },
               x = this.pattern.length;
             if (x > 32) {
-              for (var L = 0, S = x % 32, w = x - S; L < w; )
+              for (var L = 0, S = x % 32, w = x - S; L < w;)
                 (b(this.pattern.substr(L, 32), L), (L += 32));
               if (S) {
                 var _ = x - 32;
@@ -699,15 +699,15 @@ var e, t;
                           ignoreLocation: p,
                         });
                         if (((x = Math.min(O, x)), (S = m + k), w))
-                          for (var j = 0; j < k; ) ((_[m + j] = 1), (j += 1));
+                          for (var j = 0; j < k;) ((_[m + j] = 1), (j += 1));
                       }
                       S = -1;
                       for (
                         var I = [], C = 1, E = k + M, $ = 1 << (k - 1), P = 0;
                         P < k;
                         P += 1
                       ) {
-                        for (var N = 0, D = E; N < D; ) {
+                        for (var N = 0, D = E; N < D;) {
                           var z = R(t, {
                             errors: P,
                             currentLocation: b + D,
@@ -1232,13 +1232,13 @@ var e, t;
           i < o;
           i += 1
         ) {
-          for (var c = n[i], a = !1, s = -1; !a && ++s < H; ) {
+          for (var c = n[i], a = !1, s = -1; !a && ++s < H;) {
             var u = G[s],
               h = u.isMultiMatch(c);
             h && (r.push(new u(h, t)), (a = !0));
           }
           if (!a)
-            for (s = -1; ++s < H; ) {
+            for (s = -1; ++s < H;) {
               var f = G[s],
                 l = f.isSingleMatch(c);
               if (l) {

docs/deps/search-1.0.0/mark.min.js

@@ -930,7 +930,7 @@
             value: function (e) {
               if (e) {
                 if (3 === e.nodeType)
-                  for (; e.nextSibling && 3 === e.nextSibling.nodeType; )
+                  for (; e.nextSibling && 3 === e.nextSibling.nodeType;)
                     ((e.nodeValue += e.nextSibling.nodeValue),
                       e.parentNode.removeChild(e.nextSibling));
                 else this.normalizeTextNode(e.firstChild);

tests/testthat/test-conversion.R

@@ -11,7 +11,6 @@ test_that("convert human to mouse with valid gene symbols", {
 })
 
 
-
 ad <- spe_to_ad(spe, assay = "counts")
 
 test_that("spe_to_ad returns an AnnData object", {

tests/testthat/test-signature.R

@@ -21,7 +21,6 @@ test_that("Immunedeconv models works", {
 })
 
 
-
 # Test for input validation in build_model
 test_that("build_model requires non-null single_cell_obj", {
   expect_error(build_model(NULL, method = "rctd"), "Parameter 'single_cell_obj' missing or null, but is required")

tests/testthat/test-utils.R

@@ -14,7 +14,6 @@ testthat::test_that("subsetSCE subsets the SingleCellExperiment correctly", {
 })
 
 
-
 testthat::test_that("Normalization works", {
   normalized <- spacedeconv::normalize(sce, method = "cpm", assay = "counts")
 

tests/testthat/test-visualization.R

@@ -23,8 +23,6 @@ test_that("Plot Umi Count works", {
 })
 
 
-
-
 test_that("Plot_post_abundant works", {
   p <- plot_most_abundant(spe, method = "estimate")
 

tests/testthat/tmpdir/test-model_and_deconvolute.R

@@ -2,8 +2,6 @@ spe <- readRDS(system.file("testdata", "spe.rds", package = "spacedeconv"))
 sce <- readRDS(system.file("testdata", "sce.rds", package = "spacedeconv"))
 
 
-
-
 test_that("quanTIseq model and deconvolution in one step works", {
   deconv <- spacedeconv::build_and_deconvolute(
     single_cell_obj = sce,