Quality Control Analysis - after QC

Microglia data

255 samples (from 314) | Different brain regions from the same donor | Multi disease cohort.

expression_dir = "~/ad-omics_hydra/microglia_omics/expression_tables/added_pilot_314s/expr_4brain_regions/"
work_plots = "~/pd-omics/katia/scripts/GitHub_scripts/glia_omics/3rd_pass_mic_255s/"
marker_folder = "~/pd-omics/katia/Microglia/markers_genes/"

Gene markers

load(paste0(expression_dir, "Expression_filt_255s.Rdata"))

markers_file = paste0(marker_folder, "markers.xlsx")
markers = read_excel(markers_file, sheet = "markers_pilot", col_names = TRUE) 
markers = as.data.frame(markers)

marker_expression = merge(genes_tpm_exp_3rd, markers, by.x = 0, by.y = "ensembl", sort = F)
# dim(marker_expression)
# head(marker_expression)

rownames(marker_expression) = marker_expression$gene_name
cell_type = marker_expression$cell_type  # keep in same gene order 
marker_expression$gene_name = NULL 
marker_expression$Row.names = NULL
marker_expression$cell_type = NULL

marker_expression = as.matrix(log2(marker_expression + 1))

Hm: from pilot list

# Create the heatmap annotation
cell_type = as.factor(cell_type)
# cell_type_colors <- data.frame(cell_type = levels(cell_type), color = I(brewer.pal(nlevels(cell_type), name = 'Dark2')))
cell_type_colors <- data.frame(cell_type = levels(cell_type), color = pal_lancet('lanonc')(nlevels(cell_type)))
cell_type_df = left_join(data.frame(cell_type = cell_type), cell_type_colors, by="cell_type")
res <- unlist(lapply(split(cell_type_colors$color, cell_type_colors$cell_type), unlist))
row_ha = rowAnnotation(`Cell Type` = as.factor(cell_type_df$cell_type), col = list(`Cell Type` = res), show_annotation_name = F)

# pdf(paste0(work_plots, "HM_markers_255s.pdf"), width = 10, height = 6)
colPalette <- colorRampPalette(rev(brewer.pal(10, "RdYlBu")))(256)
Heatmap(marker_expression,
        col = colPalette,
        name = "log2(TPM+1)", # Legend title
        cluster_rows = T,
        #  row_names_gp = gpar(fontsize = 6), # Text size for row names)
        show_column_dend = F, 
        show_column_names = F, 
        right_annotation = row_ha)
#dev.off()