wrapperMixModelsUmap

This function executes a ubuntu docker that performs wrapperMixModelsUmap

wrapperMixModelsUmap(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  geneList,
  separator,
  k,
  seed,
  epochs,
  finalName,
  maxit = 10000
)

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 count matrix

geneList,

a character string indicating the path of the geneList matrix (no header, no row names)

separator,

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

k,

number of soft labels to divide the density

seed,

number for reproducibility

epochs,

epochs number for umap algorithm

finalName,

name for output files

maxit,

number of max iteration for mixmodels

Value

plot

Author

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

Examples

if (FALSE) {
dir.create("scratch")
wrapperMixModelsUmap(group=c("docker"), scratch.folder=paste(getwd(),"/scratch",sep=""), file=paste(getwd(),"/setA.csv",sep=""),separator=",",seed=111,epochs=1000,k=3,finalName="prova",geneList=paste(getwd(),"/geneList.csv",sep=""))
}