vioHTMLByGenes

The present function plot count matrix data into a vioplot for a gene in each cluster. I requires two file the count matrics and the _clustering.output file.

vioHTMLByGenes(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  separator,
  cl,
  gene,
  logtwo
)

Arguments

group,

a character string. Two options: sudo or docker, depending to which group the user belongs

scratch.folder,

a character string indicating the path of the scratch folder

file,

a character string indicating the path of the file, with file name and extension included

separator,

separator used in count file, e.g. '\t', ','

cl,

Clustering.output file, which contains the output of every clustering algorithm embedded in rCASC or it can be a file having in the first column cells names and in the second column cluster to which the cell belongs. Full path is required.

gene,

gene name that wants to be inspected. Gene format depends from the rows names format of the count file.

logtwo,

1 if the matrix is already in log2, 0 otherwise

Author

Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino

Examples

if (FALSE) {
 vioHTMLByGenes(group=c("sudo"), scratch.folder="/home/lucastormreig/genesPlot/test/scratch", file="/home/lucastormreig/genesPlot/test/data/setA.csv",separator=",", cl="/home/lucastormreig/genesPlot/test/data/setA_clustering.output.csv",gene="ARF5",logtwo=1)
}