plot_cpdb3: Plotting CellPhoneDB results as a chord diagram

In zktuong/ktplots: Plot single-cell data dotplots

Plotting CellPhoneDB results as a chord diagram

Description

Plotting CellPhoneDB results as a chord diagram

Usage

plot_cpdb3(
  scdata,
  cell_type1,
  cell_type2,
  celltype_key,
  means,
  pvals,
  deconvoluted,
  keep_significant_only = TRUE,
  splitby_key = NULL,
  standard_scale = TRUE,
  gene_symbol_mapping = NULL,
  frac = 0.1,
  remove_self = TRUE,
  desiredInteractions = NULL,
  degs_analysis = FALSE,
  directional = 1,
  alpha = 0.5,
  edge_colors = NULL,
  grid_colors = NULL,
  show_legend = TRUE,
  legend.pos.x = 20,
  legend.pos.y = 20,
  return_df = FALSE,
  plot = TRUE,
  ...
)

Arguments

scdata	single-cell data. Must be a SingleCellExperiment object.
cell_type1	cell type 1
cell_type2	cell type 2
celltype_key	vector holding the celltype_key for each cell or column name of scdata's metadata. MUST match cpdb's columns
means	object holding means.txt from cpdb output
pvals	object holding pvals.txt from cpdb output
deconvoluted	object holding deconvoluted.txt from cpdb output
keep_significant_only	logical. Default is FALSE. Switch to TRUE if you only want to plot the significant hits from cpdb.
splitby_key	column name in the metadata/coldata table to split the spots by. Can only take columns with binary options. If specified, name to split by MUST be specified in the meta file provided to cpdb prior to analysis.
standard_scale	logical. scale the expression to range from 0 to 1. Default is TRUE
gene_symbol_mapping	default = NULL.column name for rowData in sce holding the actual gene symbols if row names aren't gene symbols
frac	default = 0.1. Minimum fraction of celtypes expressing a gene in order to keep the interaction. Gene must be expressesd >= 'frac' in either of the pair of celltypes in order to keep.
remove_self	default = TRUE. Remove self-self arcs.
desiredInteractions	default = NULL. Specific list of celltype comparisons e.g. list(c('CD4_Tcm', 'cDC1'), c('CD4_Tcm', 'cDC2')). Also accepts a dataframe where first column is celltype 1 and 2nd column is celltype 2.
degs_analysis	if is CellPhoneDB degs_analysis mode.
directional	Whether links have directions. 1 means the direction is from the first column in df to the second column, -1 is the reverse, 0 is no direction, and 2 for two directional.
alpha	transparency for links
edge_colors	vector of colors for links
grid_colors	vector of colors for grids
show_legend	whether or not to show the legend
legend.pos.x	x position of legend
legend.pos.y	y position of legend
return_df	logical. Default is FALSE. If TRUE, returns the data as an edge list.
plot	logical. Default is TRUE. If FALSE, the final data used to plot the chord diagram is returned.
...	passes arguments plot_cpdb

Value

Plotting CellPhoneDB results as a CellChat inspired chord diagram

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