featurePlot: Visualize 'Pathways or Terms' on a dimensional reduction plot

In guokai8/scGSVA: GSVA and UCell signature enrichment analysis for single cell RNA seq

Visualize 'Pathways or Terms' on a dimensional reduction plot

Description

Colors single cells on a dimensional reduction plot according to a 'pathways' (i.e. KEGG, GO terms)

Usage

featurePlot(
  object,
  features,
  reduction = "umap",
  color = NULL,
  group_by = NULL,
  label = NULL,
  dims = c(1, 2),
  pt.size = 1,
  pt.shape = 19,
  min.cutoff = NA,
  max.cutoff = NA,
  nrow = NULL,
  ncol = NULL,
  basesize = 12,
  label.size = 4,
  label.color = "black"
)

Arguments

object	A GSVA objectect or data.frame
features	A vector of features to plot,
reduction	Which dimensionality reduction to use. default("umap")
color	Colors to use for identity class plotting
group_by	Name of one or more metadata columns to group (color) cells by
label	Name of one or more metadata columns to label the cells by
dims	Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions
pt.size	Size of the points on the plot
pt.shape	If NULL, all points are circles (default)
min.cutoff	max.cutoff Vector of minimum and maximum cutoff values for each feature, may specify quantile in the form of 'q##' where is the quantile (eg, 'q1', 'q10')
nrow	Number of rows
ncol	Number of columns
basesize	base font size, given in pts.
label.size	Sets the size of the labels
label.color	Sets the color of the label text

Author(s)

Kai Guo

Examples

set.seed(123)
library(scGSVA)
data(pbmc_small)
hsko<-buildAnnot(species="human",keytype="SYMBOL",anntype="KEGG")
res<-scgsva(pbmc_small,hsko)
featurePlot(res,features="Wnt.signaling.pathway")

guokai8/scGSVA documentation built on Nov. 15, 2024, 12:54 a.m.