integrationCircos: integrationCircos

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

integrationCircos

Description

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

Usage

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(s)

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

Examples

## Not run: 
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"
)


## End(Not run)

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