geneDotPlot: Plotting genes as dotplot

In zktuong/ktplots: Plot single-cell data dotplots

Plotting genes as dotplot

Description

Plotting genes as dotplot

Usage

geneDotPlot(
  scdata,
  celltype_key,
  genes,
  splitby_key = NULL,
  pct.threshold = 0.05,
  scale = NULL,
  standard_scale = NULL,
  keepLevels = TRUE,
  save.plot = FALSE,
  h = 5,
  w = 5,
  filepath = NULL,
  filename = NULL,
  heat_cols = NULL,
  col_limits = NULL,
  fill = FALSE,
  outline_col = "black",
  outline_size = 0.2
)

Arguments

scdata	single-cell data. can be seurat/summarizedexperiment object
celltype_key	column name holding the celltype for each cell
genes	genes you want to plot
splitby_key	column name in the metadata/coldata table to split the spots by. If not provided, it will plot via celltype_key provided.
pct.threshold	float. required to keep gene expressed by minimum percentage of cells
scale	logical. scale the expression to mean +/- SD. NULL defaults to TRUE.
standard_scale	logical. scale the expression to range from 0 to 1. NULL defaults to FALSE.
keepLevels	logical. keep the original factor of the levels of the celltype_key (for plotting)
save.plot	logical. will try to save the pdf
h	height of plot
w	width of plot
filepath	path to file, or path to folder
filename	path to file
heat_cols	colour gradient for the dot plot
col_limits	set limits to the color gradient
outline_col	colour of outlines if fill = TRUE
outline_size	stroke size of outlines if fill = TRUE

Value

ggplot dot plot object of selected genes

Examples

data(kidneyimmune)
geneDotPlot(kidneyimmune, genes = c("CD68", "CD80", "CD86", "CD74", "CD2", "CD5"), celltype_key = "celltype", splitby_key = "Project", standard_scale = TRUE) + theme(strip.text.x = element_text(angle = 45, hjust = 0))

zktuong/ktplots documentation built on April 12, 2025, 9:53 p.m.