UTUC_plotting/scRNA_panel_plotting.R at main · Hoho1996/UTUC_plotting · GitHub

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library(ggplot2)
library(dplyr)
library(ggrepel)
library(scales)

theme_plot <- theme_classic(base_size = 12) +
  theme(
    axis.text = element_text(color = "black"),
    axis.title = element_text(color = "black"),
    legend.text = element_text(color = "black"),
    legend.title = element_text(color = "black")
  )

## UMAP colored by annotated cell type
df_umap_label <- df_umap %>%
  group_by(celltype) %>%
  summarise(
    UMAP_1 = median(UMAP_1, na.rm = TRUE),
    UMAP_2 = median(UMAP_2, na.rm = TRUE),
    .groups = "drop"
  )

p_umap <- ggplot(df_umap, aes(x = UMAP_1, y = UMAP_2, color = celltype)) +
  geom_point(size = 0.25, alpha = 0.85) +
  geom_text_repel(
    data = df_umap_label,
    aes(label = celltype),
    color = "black",
    size = 3,
    show.legend = FALSE
  ) +
  labs(x = "UMAP 1", y = "UMAP 2", color = NULL) +
  theme_plot +
  theme(axis.text = element_blank(), axis.ticks = element_blank())

ggsave("scRNA_UMAP_by_celltype.pdf", p_umap, width = 5, height = 4)


## Cell-type proportions in each sample, split by SNF subtype
p_sample_celltype_proportion <- ggplot(df_proportion_long) +
  geom_col(aes(x = Sample_ID, y = proportion, fill = celltype), width = 0.9) +
  facet_grid(~ SNF_group, scales = "free", space = "free_x") +
  scale_y_continuous(labels = percent_format()) +
  labs(x = NULL, y = "Proportion", fill = NULL) +
  theme_plot +
  theme(
    axis.text.x = element_text(angle = 45, hjust = 1, size = 8),
    strip.background = element_rect(fill = "grey85", color = NA)
  )

ggsave("scRNA_sample_celltype_proportion.pdf", p_sample_celltype_proportion, width = 8, height = 4)


## Cell-type composition by SNF subtype
p_snf_celltype_distribution <- ggplot(df_cell_types_distribution) +
  geom_bar(aes(y = SNF_group, fill = celltype), position = "fill", width = 0.75) +
  scale_x_continuous(labels = percent_format()) +
  labs(x = "Percentage", y = NULL, fill = NULL) +
  theme_plot +
  theme(axis.ticks.y = element_blank())

ggsave("scRNA_celltype_distribution_by_SNF.pdf", p_snf_celltype_distribution, width = 4.5, height = 3)