plot_cpdb2: Plotting CellPhoneDB results

In zktuong/ktplots: Plot single-cell data dotplots

Plotting CellPhoneDB results

Description

Plotting CellPhoneDB results

Usage

plot_cpdb2(
  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,
  interaction_grouping = NULL,
  edge_group_colors = NULL,
  node_group_colors = NULL,
  degs_analysis = FALSE,
  return_df = FALSE,
  plot_score_as_thickness = TRUE,
  ...
)

Arguments

scdata	single-cell data. Must be SingleCellExperiment object
cell_type1	cell type 1
cell_type2	cell type 2
celltype_key	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.
interaction_grouping	default = NULL. dataframe specifying groupings of CellPhoneDB interactions. First column must be CellPhoneDB's interacting_pair column. second column is whatever grouping you want.
edge_group_colors	default = NULL. vector for colour mapping for edge groups. only used if splitby_key is specified.
node_group_colors	default = NULL. vector for colour mapping for node labels.
degs_analysis	if is CellPhoneDB degs_analysis mode.
return_df	whether to just return this as a data.frame rather than plotting iot
plot_score_as_thickness	logical. Whether to scale the thickness of the edges to the interaction score and scale alpha to -log10(significance). Default is TRUE. FALSE will be opposite behaviour
...	passes arguments plot_cpdb

Value

Plotting CellPhoneDB results as a weird chord diagram

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