plotSeurat: plotSeurat

In wguo-research/scCancer: A package for automated processing of single cell RNA-seq data in cancer

plotSeurat

Description

Construct and save plots of Seurat analysis.

Usage

plotSeurat(
  expr,
  cell.annotation = cell.annotation,
  show.features = NULL,
  bool.add.features = T,
  coor.names = c("tSNE_1", "tSNE_2"),
  bool.plotHVG = T,
  bool.runDiffExpr = T,
  diff.expr.genes = NULL,
  n.markers = 5,
  species = "human",
  savePath
)

Arguments

expr	A Seurat object.
cell.annotation	A data.frame of cells' annotation.
show.features	A list or vector for genes to be plotted in 'markerPlot'.
bool.add.features	A logical value indicating whether to add default features to 'show.features' or not.
coor.names	A vector indicating the names of two-dimension coordinate used in visualization.
bool.plotHVG	A logical value indicating Whehter to plot highly variable genes.
bool.runDiffExpr	A logical value indicating whether to perform differential expressed analysis.
diff.expr.genes	A data.frame of differential expressed genes.
n.markers	An integer indicating the number of differential expressed genes showed in the plot. The defalut is 5.
species	A character string indicating what species the sample belong to. Only "human"(default) or "mouse" are allowed.
savePath	A path to save the results files. If NULL, the 'statPath' will be used instead.

Value

A list of all plots generated by Seurat analyses.

wguo-research/scCancer documentation built on May 26, 2024, 9:12 p.m.