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process_12_monocytes.R
69 lines (45 loc) · 2.73 KB
/
process_12_monocytes.R
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library(Seurat)
library(stringr)
library(data.table)
library(tidyverse)
library(ggplot2)
library(cowplot)
library("xlsx")
library(clusterProfiler)
library(org.Hs.eg.db)
setwd("/mnt/f/dev/data/Rprojs/covidSC")
readRDS("obj.monocytes_fine_12.Rds")
deResTT_mc_fine = makeDEResults(obj.monocytes_fine_12, assay="RNA", test="t")
exprdfTT_mc_fine = getDEXpressionDF(obj.monocytes_fine_12, deResTT_mc_fine, assay="RNA")
write.table(exprdfTT_mc_fine, "monocytes_fine.de.t.tsv", sep="\t", row.names=F, quote = F)
system("rm analyseMarkers.py")
system("wget https://raw.githubusercontent.com/mjoppich/scrnaseq_celltype_prediction/master/analyseMarkers.py")
system("/usr/bin/python3 analyseMarkers.py --expr-mean mean.cluster --expressing-cell-count anum.cluster --cluster-cell-count num.cluster --organs \"Immune system\" --markers monocytes_fine.de.t.tsv --seurat")
DefaultAssay(obj.monocytes_fine_12) = "RNA"
FeaturePlot(obj.monocytes_fine_12, features = c("FCGR3A", "CD14"), pt.size = 0.01, label=T)
RidgePlot(obj.monocytes_fine_12, features = c("FCGR3A", "CD14"))
#The classical monocyte is characterized by high level expression of the CD14 cell surface receptor
#(CD14++ FCGR3A− monocyte)
# all, except 9,11,3,13
#The non-classical monocyte shows low level expression of CD14 and additional co-expression of the FCGR3A receptor
#(CD14+FCGR3A++ monocyte).
# monocytes_3
FeaturePlot(obj.monocytes_fine_12, features = c("FCGR3A", "CD14"), slot = "data", pt.size = 0.01, label=T)
idents.ncmc = c("monocytes_3")
cells_ncmc = makeGrpCells(obj.monocytes_fine_12, idents.ncmc)
idents.cmc = setdiff(setdiff(unique(obj.monocytes_fine$sub_cluster_monocytes), idents.ncmc), c("monocytes_11", "monocytes_12", "monocytes_9", "monocytes_3"))
cells_cmc = makeGrpCells(obj.monocytes_fine_12, idents.cmc)
de.ncmc_cmc = compareCells(obj.monocytes_fine_12, cells_ncmc, cells_cmc, "ncmc", "cmc")
#logfc > 0 => more in ncmc than in cmc
deResList = list("ncmc_cmc"=de.ncmc_cmc)
write.xlsx(de.ncmc_cmc, file = "todoplots/ncmc/de.ncmc_cmc.xlsx" )
saveRDS(deResList, "ncmc_cmc_monocytes.Rds")
#Rscript raAnalysis.R "ncmc_cmc_monocytes.Rds" "go_universe.Rds" "human"
#Rscript goAnalysis.R "ncmc_cmc_monocytes.Rds" "go_universe.Rds"
#Rscript gseAnalysis.R "ncmc_cmc_monocytes.Rds"
ncmc_cmc_monocytes.ra = readRDS("ra.ncmc_cmc_monocytes.Rds")
ncmc_cmc_monocytes.go = readRDS("go.ncmc_cmc_monocytes.Rds")
ncmc_cmc_monocytes.gse = readRDS("gse.ncmc_cmc_monocytes.Rds")
t=makePlotsListsGO(ncmc_cmc_monocytes.go, deResList, "todoplots/ncmc/go/")
t=makePlotsListsGO(ncmc_cmc_monocytes.ra, deResList, "todoplots/ncmc/ra/", name.ggo=NULL, name.ego="rao", name.ego_up="rao_up", name.ego_down="rao_down", name.title="ReactomePA")
t=makePlotsListsGSE(ncmc_cmc_monocytes.gse, deResList, "todoplots/ncmc/gse/")