spatialFeaturePlot: Visualize 'Pathways or Terms' on a Spatial plot

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

Visualize 'Pathways or Terms' on a Spatial plot

Description

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

Usage

spatialFeaturePlot(
  object,
  features,
  images = NULL,
  color = NULL,
  label = NULL,
  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	Name of the feature to visualize.
images	Name of the images to use in the plot(s)
color	Colors to use for identity class plotting
label	Name of one or more metadata columns to label the cells by
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)
library(Seurat)
library(SeuratData)
InstallData("stxBrain")
brain <- LoadData("stxBrain", type = "anterior1")
hsko<-buildAnnot(species="human",keytype="SYMBOL",anntype="KEGG")
res<-scgsva(brain,hsko)
spatialFeaturePlot(res,features="Wnt.signaling.pathway")

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