Survplot_genedata: Survival K-M plot base on expression matrix and design object

In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

Description

Survplot.genedata help draw KM plot base on expression matrix and design object

Usage

Survplot_genedata(expr.matrix, design, select, event.status, event.time,
  event.lower = 0, mode = c("median", "maxstat")[2],
  pval.position = NULL, size = 12, save.file = F, show.music = F,
  width = 12, height = 12, names = "love")

Arguments

expr.matrix	expression matrix
design	design object
select	the genes or markers you want to select
event.status	the colname of the status of event.
event.lower	the lower cutoff of event time.Default is 0.
mode	the mode of cut-off strategy for continuous value like gene expression data.Default is mode = "maxstat" provided by maxstat.test.If you want median value as cut-off,you can just set mode = "median"
pval.position	the postion of p value in the plot
size	the size of saved plot
save.file	whether to save pdf for plot.If you select more than 1 genes,it would set save.file = T automatically.
show.music	whether to show music when job was completed.Only available when you select more than 1 genes.
width	the width of saved plot
height	the height of saved plot
event.timethe	colname of the time of event.
part	name of saved pdf file

Details

There are some different between the output of multi- and uni- variate plot.

Author(s)

Weibin Huang<[e-mail]>

See Also

maxstat.test

Examples

library(lucky);
data("rna.tpm",package = "lucky")
data("rna.design",package = "lucky")

## Muti-variable Plot.here I focus on patients with more follow-up time than 89 days with event.lower = 89
p <- Survplot_genedata(expr.matrix = log2(rna.tpm + 1),
                       design = rna.design,
                       select = c("ENSG00000004478",
                                  "ENSG00000000457"),
                       event.status = "OS.status",
                       event.time = "OS.time",
                       event.lower = 89,
                       mode = c("median","maxstat")[2],
                       pval.position = c(900,1),# x=900,y=1
                       size = 12,
                       save.file = F,
                       show.music = F,
                       width = 12,height = 12,
                       names = "love")

## univariable Plot
p <- Survplot_genedata(expr.matrix = log2(rna.tpm + 1),
                       design = rna.design,
                       select = "ENSG00000004478",
                       event.status = "OS.status",
                       event.time = "OS.time",
                       event.lower = 89,
                       mode = c("median","maxstat")[2],
                       pval.position = c(900,1))

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.