HC - IBD label transfer

We want to compare the clusters we obtained with the two datasets:

Libraries

library(matchSCore2)
library(nnet)
library(Matrix)
library(Seurat)
library(ggplot2)

Data preparation

subsets <- c('epi', 'myeloids', 'plasmas', 'stroma', 'tcells')

for(subset in subsets){
  ref <- readRDS(paste0("~/000_GitHub/ibd-bcn_single_cell/Analysis of our data/01_Samples_by_Health/HC/annotated/", subset, ".RDS"))
  ref@active.ident <- factor(ref$annotation)
  output.seu <- FindAllMarkers(ref, only.pos = T)
  gene_cl.ref <- cut_markers(levels(output.seu$cluster),output.seu,ntop=100)
  saveRDS(gene_cl.ref, file = paste0("~/000_GitHub/ibd-bcn_single_cell/Analysis of our data/01_Samples_by_Health/HC/annotated/genes/",subset,"_gene_cl.ref.RDS"))
}

for(subset in subsets){
  ref <- readRDS(paste0("~/000_GitHub/ibd-bcn_single_cell/Analysis of our data/01_Samples_by_Health/IBD/annotated/", subset, ".RDS"))
  ref@active.ident <- factor(ref$annotation)
  output.seu <- FindAllMarkers(ref, only.pos = T)
  gene_cl.ref <- cut_markers(levels(output.seu$cluster), output.seu, ntop=100)
  saveRDS(gene_cl.ref, file = paste0("~/000_GitHub/ibd-bcn_single_cell/Analysis of our data/01_Samples_by_Health/IBD/annotated/genes/",subset,"_gene_cl.ref.RDS"))
}

Jaccard indexes

for(subset in subsets){
  ibd <- readRDS(file = paste0("~/000_GitHub/ibd-bcn_single_cell/Analysis of our data/01_Samples_by_Health/IBD/annotated/genes/",
                               subset,
                               "_gene_cl.ref.RDS"))
  hc <-  readRDS(file = paste0("~/000_GitHub/ibd-bcn_single_cell/Analysis of our data/01_Samples_by_Health/HC/annotated/genes/",
                               subset,
                               "_gene_cl.ref.RDS"))
  ms <- matchSCore2(gene_cl.ref = hc,
                    gene_cl.obs = ibd,
                    ylab = "IBD",
                    xlab = "HC")
  ms$ggplot$layers[[2]]$aes_params$size <- 3
  j <- ms$ggplot +
    theme(axis.text.x = element_text(angle=90,
                                     vjust = 0.5, size = 9),
          axis.text.y = element_text(size = 9))
  cat("## ", subset, "\n"); print(j); cat("\n\n")
}

epi

myeloids

plasmas

stroma

tcells

```