find_cluster_markers: Find and plot top n DEGs per cluster

Description

This function uses Seurat's marker finding capability to find DEGs of each cluster

Usage

find_cluster_markers(
  so_clone,
  type,
  logfc.threshold = 0.2,
  min.pct = 0,
  only.pos = TRUE,
  n_markers = 5,
  value = "log2_expr",
  text_size = 16,
  title_size = 18,
  legend_size_pt = 4,
  p_val_thresh = 0.05,
  bin = TRUE,
  plot_directory = None
)

Value

A list object with cluster marker information markers_clone = data.table of all cluster markers top_markers_clone = data.table of just top cluster markers top_clone_vis = data.frame formatted for plot visualization of top cluster markers

Arguments

so_clone: seurat object with 'clone' (SlideCNA-designated cluster) and bin annotations
type: character string that is 'all' if using malignant and normal clusters and 'malig' if just using malignant clusters
logfc.threshold: numeric float that is seurat parameter, representing the minimum log2 fold change for DEGs to be significant
min.pct: numeric Seurat function parameter
only.pos: TRUE if only using DEGs with positive log2 fold change
n_markers: integer of number of top DEGs to plot/use
value: expression value of DEGs; one of ("log2_expr", "avg_expr", and "avg_log2FC") for log2-normalized aerage epxression, average expression, or log2 fold change
text_size: Ggplot2 text size
title_size: Ggplot2 title size
legend_size_pt: Ggplot2 legend_size_pt
p_val_thresh: value for p value cutoff for DEGs
bin: TRUE if using binned beads
plot_directory: output plot directory path