Hi,

I was working on marking genes of interest on the heatmap via ComplexHeatmap R package. Instead of specifying row numbers in anno_mark function, I specified a vector of genes to mark on the heatmap (see below) and used a combination of which() and %in% to isolate the row indices that match the gene character vector. It seems like the order of line marking differs compared to row labels (example screenshot below). Please assist how to resolve this issue? Why does the order differ. I am working with 500 diff.exp genes, hence I need to mark atleast 30 genes.

Thank you,

Toufiq

Genes to be marked

genes_to_show <- c("C4orf54", "CCN1", "ADAMTS4", "ARX", "CORO1A", "CMC4", "CDH11", "CCDC102B", "CRYAB", "CCN2")
mark_at = which(rownames(matrix) %in% genes_to_show)
ha = rowAnnotation(foo = anno_mark(at = mark_at, labels = genes_to_show))

Plot

library(ComplexHeatmap)
pdf("Heatmap.pdf",height = 10, width = 7)
Heatmap(matrix, 
        name = "Z-score - log2CPM", 
        col = circlize::colorRamp2(c(-2, 0, 2), c("cyan", "black", "yellow")),
        na_col = "grey",
        cluster_rows = T,
        cluster_columns = F,
        top_annotation = column_ha,
        right_annotation = ha,
        column_split = Sample_metadata$Category,
        row_names_max_width = unit(10,"in"),
        row_title_gp = gpar(fontsize = 15),
        column_title_gp = gpar(fontsize = 20),
        column_names_gp = gpar(fontsize =10),
        row_names_gp = gpar(fontsize =3),
        show_column_names = T)
dev.off()