Fullplot_v2: Fullplot_v2

In chenweng1991/EZsinglecell:

Description

This function plot basic clustering result for seurat object

Usage

Fullplot_v2(object, name, topgene = NULL, resolusion = "res.0.6",
  signiture = c("INS", "GCG", "SST", "PPY", "KRT19", "COL1A2", "REG1A",
  "DNAJB1", "GHRL"), p.tsnecluster = T, Pheatmap = T,
  p.tsnesample = T, p.pcacluster = T, p.pcasample = T,
  darwPCdrive = T, cell.use = 500, color = "Paired", PC34 = F,
  dotsize = 0.1, heatmapannosize = 0.5, doreturn = F, pdfwidth = 7,
  pdfheight = 7)

Arguments

object	The seurat object that has been analyzed.
name	the name for pdf file
topgene	An optional input of cluster marker genes if "Gettopgenes" has been run outside. This can help to save some time
resolusion	This is clustering resolution used in clustering, which can be found in [e-mail]
signiture	a vector of gene names that are intersting to be checked on tsne by color intensity
p.tsnecluster	if true, plot the tsne figure stained by clusters
Pheatmap	if true, plot the marker gene heatmap
p.tsnesample	if true, plot the tsne figure stained by samples
p.pcacluster	if true, plot the pca12 figure stained by clusters
p.pcasample	if true, plot the pca12 figure stained by sample
darwPCdrive	if true, plot the heatmap showing the pca driving genes
cell.use	the cell number used to draw PCA driving gene plot. Default is 500
color	The color palette used for tsne and pca, default is "Paired"
PC34	If ture, also plot PCA34 additionally, default is FALSE
dotsize	The dot size for tsne and pca
doreturn	If ture, retun plot to a variable
pdfwidth	The width of pdf file. Default is 7
pdfheight	The height of pdf file. Default is 7

Value

generate a pdf, if doreturn=T then return the figures

Examples

Fullplot_v2(S7rock_1.ob,"S7rock_1.ob.pdf",topgene=NULL,resolusion="res.0.6",signiture=c("INS","GCG","SST","PPY","KRT19","COL1A2","REG1A","DNAJB1","GHRL"))

chenweng1991/EZsinglecell documentation built on July 11, 2020, 3:23 p.m.