spatial Analysis

This function analyze the data that came up from permutationClustering script with spatial transcriptomics data.

spatialAnalysis(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nCluster,
  separator,
  tissuePosition
)

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

nCluster,

Last number of cluster that has to be analyzed

separator,

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

tissuePosition,

file with tissue position name with extension

Value

stability plot for each nCluster,two files with score information for each cell for each permutation.

Author

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

Examples

if (FALSE) {
spatialAnalysis(group="sudo", scratch.folder="/scratch", file="/home/lucastormreig/newDockers/data/matrix.csv",nCluster=13,separator=",",tissuePosition="/home/lucastormreig/newDockers/data/tissue_positions_list.csv")
}