plot_cpdb_heatmap: Plotting CellPhoneDB results as a heatmap

In zktuong/ktplots: Plot single-cell data dotplots

Plotting CellPhoneDB results as a heatmap

Description

Plotting CellPhoneDB results as a heatmap

Usage

plot_cpdb_heatmap(
  pvals,
  cell_types = NULL,
  degs_analysis = FALSE,
  log1p_transform = FALSE,
  show_rownames = TRUE,
  show_colnames = TRUE,
  scale = "none",
  cluster_cols = TRUE,
  cluster_rows = TRUE,
  border_color = "white",
  fontsize_row = 11,
  fontsize_col = 11,
  family = "Arial",
  main = "",
  treeheight_col = 0,
  treeheight_row = 0,
  low_col = "dodgerblue4",
  mid_col = "peachpuff",
  high_col = "deeppink4",
  alpha = 0.05,
  return_tables = FALSE,
  symmetrical = TRUE,
  default_sep = "\\|",
  ...
)

Arguments

pvals	Dataframe corresponding to 'pvalues.txt' or 'relevant_interactions.txt' from CellPhoneDB.
cell_types	vector of cell types to plot. If NULL, all cell types will be plotted.
degs_analysis	Whether 'CellPhoneDB' was run in 'deg_analysis' mode
log1p_transform	Whether to log1p transform the output.
show_rownames	whether to show row names.
show_colnames	whether to show column names.
scale	scaling mode for pheatmap.
cluster_cols	whether to cluster columns.
cluster_rows	whether to cluster rows.
border_color	border color.
fontsize_row	row font size.
fontsize_col	column font size.
family	font family.
main	plot title.
treeheight_col	height of column dendrogram.
treeheight_row	height of row dendrogram.
low_col	low colour for heatmap.
mid_col	middle colour for heatmap.
high_col	high colour for heatmap.
alpha	pvalue threshold to trim.
return_tables	whether or not to return the results as a table rather than the heatmap
symmetrical	whether or not to return as symmetrical matrix
default_sep	the default separator used when CellPhoneDB was run.
...	passed to pheatmap::pheatmap.

Value

pheatmap object of cellphone db output

Examples

data(kidneyimmune)
data(cpdb_output2)
plot_cpdb_heatmap(pvals2)

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