find_cluster_markers: Find and plot top n DEGs per cluster

In dkzhang777/SlideCNA: Calls Copy Number Alterations from Slide-Seq Data

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
)

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

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

dkzhang777/SlideCNA documentation built on Jan. 25, 2025, 5:53 p.m.