integrationCircos

This function executes integrationCircos, which plots the integrated results of the analysis performed with gseaXLmHG, seuratIntegrationPermutation, integrationPsblk, integrationPblkae and BC

integrationCircos(
  group = c("sudo", "docker"),
  scratch.folder,
  gsea.file = NULL,
  isc.file = NULL,
  XYpb.file = NULL,
  pblkae.file = NULL,
  bcsc.file = NULL,
  Xcls.groups = NULL,
  Ycls.groups = NULL,
  outputFolder
)

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

gsea.file,

a character string indicating the path of the final_score.csv generated with gseaXLmHG, file, with file name and extension included.

isc.file,

a character string indicating the path of the final_score.csv generated with seuratIntegrationPermutation, file, with file name and extension included. included.

XYpb.file,

a character string indicating the path of the final_score.csv generated with integrationPsblk, file, with file name and extension included.

pblkae.file,

a character string indicating the path of the final_score.csv generated with integrationPblkae, file, with file name and extension included.

bcsc.file,

a character string indicating the path of the FINAL_score.csv generated with BCscWrapper, file, with file name and extension included.

Xcls.groups,

a vector of strings describing the groups of more similar clusters. The optimal order of the clusters can be deduced by the output of integrationPblkae function with the option type="intra". Format: c("1cl6", "1cl2-1cl3", "1cl1-1cl4-1cl5").

Ycls.groups,

a vector of strings describing the order of the clusters. The optimal order of the clusters can be deduced by the output of integrationPblkae function with the option type="intra". Format: c("2cl1-2cl3", "2cl2-2cl4", "2cl5-2cl6")

outputFolder,

where results are placed

Value

A picture called integrated_score.png and a file called integrated_score.csv and all the final_scores.csv used to produce the integrated results. The colour ramp for Xgroups is yellow-magenta as instead for the Ygroups is green-blue. Clusters sharing the same colors are those characterized by belonging to the same subgroup detected using integrationPblkae with type="intra". Picture and data used for the integration are lccated in integrated_score folder. Inter cluster edges color code: 1 red; 1-0.7 green; 0.7-0.5 blue; 0.5-0.3 violet; 0.3-0.2 grey; 0.2-0 gold.

Author

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

Examples

if (FALSE) {
library(rCASC)
integrationCircos(group="docker", 
                  scratch.folder="/scratch", 
                  gsea.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/GSEA/final_score.csv",
                  isc.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/ISC/final_score.csv",
                  XYpb.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/XYpb/XYpb_final_score.csv",
                  pblkae.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/pblkAE/final_score.csv",
                  bcsc.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/BCsc/FINAL_score.csv",
                  Xcls.order=NULL,
                  Ycls.order=NULL, 
                  outputFolder="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2"
)

integrationCircos(group="docker", 
                  scratch.folder="/scratch", 
                  gsea.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/GSEA/final_score.csv",
                  isc.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/ISC/final_score.csv",
                  XYpb.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/XYpb/XYpb_final_score.csv",
                  pblkae.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/pblkAE/final_score.csv",
                  bcsc.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/BCsc/FINAL_score.csv",
                  Xcls.groups=c("1cl6", "1cl2-1cl3", "1cl1-1cl4-1cl5"),
                  Ycls.groups=c("2cl1-2cl3", "2cl2-2cl4", "2cl5-2cl6"), 
                  outputFolder="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2"
)

}