Description Usage Arguments References Examples
View source: R/visualization.R
Function 'plotCoocMutex' plots the co-occurrence and mutual exclusivity plots for mutation genes which drive immune cells.
1 | plotCoocMutex(maffile, mutcell.summary, cellnumcuoff = 3, fontSize = 0.8)
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maffile |
The name of mutation annotation file (MAF) format data. It must be an absolute path or the name relatived to the current working directory. |
mutcell.summary |
The result of 'mutcellsummary' function |
cellnumcuoff |
A threshold value (4 as the default value). The mutation genes which drive at least "cellnumcuoff" cells are retained for drawing a co-occurrence and mutual exclusivity plots. |
fontSize |
cex for gene names. Default 0.8 |
Gerstung M, Pellagatti A, Malcovati L, et al. Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes. Nature Communications. 2015;6:5901. doi:10.1038/ncomms6901.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | # get the result of `exp2cell` funtion
cellmatrix<-GetExampleData("cellmatrix")
#get the binary mutations matrix,
mutmatrix<-GetExampleData("mutmatrix")
# get the result of `mutcorcell` funtion
mutcell<-GetExampleData("mutcell")
#perform the function mutcellsummary
summary<-mutcellsummary(mutcell = mutcell,mutmatrix = mutmatrix,cellmatrix=cellmatrix)
#dir is the name of mutation annotation file (MAF) format data.
#It must be an absolute path or the name relatived to the current working directory.
maf<-"dir"
#plot the co-occurrence and mutual exclusivity plots for mutation genes which drive immune cells.
plotCoocMutex(maffile = maf,mutcell.summary = summary,cellnumcuoff =0)
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