spatialAnalysis2: spatial Analysis Plus

In kendomaniac/rCASC: rCASC reproducible Classification Analysis of Single Cell Sequencing Data

spatial Analysis Plus

Description

This function analyzes the data that came up from permutationClustering script with spatial transcriptomics data. The function integrates CSS with a score, which is related to the beloging cluster identity of a cell with respect to the other 6 cell neighborhood that surround it.

Usage

spatialAnalysis2(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nCluster,
  separator,
  tissuePosition,
  Sp = 0.8,
  percentageIncrease = 10
)

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
Sp	Threshold to assign the plus score. 1 mean that all 6 cells, sorrounding the central cell, belong to the same cluster of the central cell. 0.8 out mean 5 out of 6 are of the same cluster of the central cell, 0.6 mean 4 out of 6 are of the same cluster of the central cell. We do not suggest to go below these three value.
percentageIncrease	percentage of the CSS score that has to be increased if the Threshold condition is satisfied.

Value

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

Author(s)

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

Examples

## Not run: 
spatialAnalysis2(group=c("sudo"), scratch.folder="/home/lucastormreig/temp/", file="/home/lucastormreig/test/spatialAnalysis/spatial/HLNrevised.csv",nCluster=5,separator=",",tissuePosition="/home/lucastormreig/test/spatialAnalysis/spatial/Results/tissue_positions_list.csv",Sp=0.8,percentageIncrease=10)

## End(Not run)

kendomaniac/rCASC documentation built on July 3, 2024, 6:05 a.m.