Description Usage Arguments Details Author(s) See Also Examples
View source: R/BI_Survplot.genedata.R
Survplot.genedata help draw KM plot base on expression matrix and design object
1 2 3 4 |
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 |
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 |
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 |
There are some different between the output of multi- and uni- variate plot.
Weibin Huang<654751191@qq.com>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | 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))
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