cnmf_programs_in_ACC

Enrichment analysis by top 200 genes of each program

plt_list = list()
for (i in 1:ncol(gep_scores)) {
  top_genes = gep_scores  %>%  arrange(desc(gep_scores[i])) #sort by score a
  top = head(rownames(top_genes),200) #take top top_genes_num
  res = genes_vec_enrichment(genes = top,background = rownames(gep_scores),homer = T,title = 
                    i,silent = T,return_all = T)
   
  plt_list[[i]] = res$plt
}
gridExtra::grid.arrange(grobs = plt_list)

score expression in all acc cancer cells

# Make metagene names
for (i in 1:ncol(all_metagenes)) {
  colnames(all_metagenes)[i] = "metagene." %>% paste0(i)
}


#add each metagene to metadata
for (i in 1:ncol(all_metagenes)) {
  metage_metadata = all_metagenes %>% select(i)
  all_acc_cancer_cells = AddMetaData(object = all_acc_cancer_cells,metadata = metage_metadata)
}

Note: Using an external vector in selections is ambiguous.
ℹ Use `all_of(i)` instead of `i` to silence this message.
ℹ See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
This message is displayed once per session.

FeaturePlot(object = all_acc_cancer_cells,features = colnames(all_metagenes))

print_tab <- function(plt,title) {
   cat("### ",title," \n")
  print(
    plt
    )
  plot.new()
  dev.off()
  cat(' \n\n')
}

Program assignment

print_tab(plt = DimPlot(object = all_acc_cancer_cells,group.by = "program.assignment",cols =colors),title = "program.assignment")

program.assignment

print_tab(plt = DimPlot(object = all_acc_cancer_cells,group.by = "patient.ident"),title = "patient.ident")

patient.ident

NA

luminal_over_myo correlation

lumScore_vs_program = FetchData(object = all_acc_cancer_cells,vars = c("lum_over_myo","program.assignment"))
lumScore_vs_program = lumScore_vs_program %>% dplyr::filter(program.assignment %in% c("metagene.1","metagene.2","metagene.4"))
plt = ggboxplot(lumScore_vs_program, x = "program.assignment", y = "lum_over_myo",
          palette = "jco",
          add = "jitter")+ stat_compare_means(method = "wilcox.test",comparisons = list(c("metagene.1","metagene.2"),c("metagene.2","metagene.4")))

print_tab(plt = FeaturePlot(object = all_acc_cancer_cells,features = "lum_over_myo"),title = "lum_over_myo")

lum_over_myo

print_tab(plt = plt,title = "wilcox")

wilcox

NA