spatialAnalysis2.Rd
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.
spatialAnalysis2( group = c("sudo", "docker"), scratch.folder, file, nCluster, separator, tissuePosition, Sp = 0.8, percentageIncrease = 10 )
group, | a character string. Two options: sudo or docker, depending to which group the user belongs |
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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. |
stability plot for each nCluster,two files with score information for each cell for each permutation.
Luca Alessandri , alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino
if (FALSE) { 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) }