DIALOGUE.plot: DIALOGUE.plot

In livnatje/DIALOGUE: DIALOGUE is a dimensionality reduction algorithm that uses cross-cell-type associations to identify multicellular programs and map the cell transcriptome as a function of its environment.

DIALOGUE.plot

Description

Plot DIALOGUE results. The resulting plots will show the cell-type-specific components of each multicellular program as a function of its other components; and the composition of each multicellular program, depicting how many of its genes are cell-type-specific, and how many are shared across multiple cell types.

Usage

DIALOGUE.plot(
  R,
  results.dir = "~/Desktop/DIALOGUE.results/",
  filename,
  pheno = NULL,
  mark.samples = NULL,
  metadata = NULL,
  d = 1,
  MCPs = 1:R$k["DIALOGUE"]
)

Arguments

R	DIALOGUE output
results.dir	the directory where the PDF figure file will be located
pheno	(optional) the name of a binary feature of interest to visualize in relation to the MCPs.

Details

In case there is a specific feature or phenotype of interest DIALOGUE will plot the MCP expression when stratifying the cells according to that classification.

Author(s)

Livnat Jerby

Examples

# Run DIALOGUE
R<-DIALOGUE.run(rA,results.dir = "~/Desktop/Results/",plot.flag = F)
# Plot the results
DIALOGE.plot(R,results.dir = "~/Desktop/Figures/",pheno = R$pheno)
# Alternatively
R<-DIALOGUE.run(rA,results.dir = "~/Desktop/Results/",plot.flag = T)

livnatje/DIALOGUE documentation built on Jan. 30, 2024, 1:31 a.m.