Fullplot_v2: Fullplot_v2

Description Usage Arguments Value Examples

View source: R/Fullplot_v2.R

Description

This function plot basic clustering result for seurat object

Usage

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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 object@data.info

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

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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.