SEplot: SEgenes plot

View source: R/Visualize.R

SEplotR Documentation

SEgenes plot

Description

Visualization of SE genes analysis

Usage

SEplot(
  object,
  diffgenes = diffgenes,
  topgenes = 100,
  method = "Integrated",
  outputFolder = NULL,
  savePlot = TRUE,
  Species = NULL,
  category = "C2",
  Geneformat = "gene_symbol",
  ...
)

Arguments

object

a giotto object

diffgenes

A list out of SE-genes calculation.

topgenes

Integer; set how many top SE-genes to take, default as 100.

method

A character to select the SE method for downstream analysis, one of "Binspect","silhouetteRank","SPARK", "SpatialDE" & "Integrated".

outputFolder

Output folder to save results.

savePlot

Boolean, whether to save plot.

Species

Species name, more details in msigdbr_species

category

MSigDB collection abbreviation, such as H or C1.

Geneformat

Format of gene name in count matrix, one of "ensembl_gene", "gene_symbol".

...

other arguments

Value

ggplot object


YeehanXiao/STREAM documentation built on Aug. 13, 2022, 6:43 p.m.