reorder group column in pheatmap

Question

[Yihan]

I'm trying to order the group of my heatmap with wildtype (WT) on the left and disease (SCA7) on the right. However, my heatmap always put SCA7 on the left and WT on the right even after setting cluster_cols to FALSE.

pheatmap(zscore, cluster_rows = FALSE, show_rownames = TRUE,
     show_colnames = FALSE, cluster_cols = FALSE, annotation_col = df,
     color = colorRampPalette(c("green","black", "red"))(100))

The df that annotation_col corresponds to looks like this, so the order is WT at first.

                      Genotype

S15_merged WT

S14_merged WT

S13_merged WT

S11_merged WT

S12_merged WT

S20_merged SCA7

S19_merged SCA7

S18_merged SCA7

S16_merged SCA7

S17_merged SCA7

[cpad0112]

Post example data and image to understand the issue better.

Answer 1

[shiyang_bio]

pheatmap will plot your data in the order of colnames(zscore) if you set cluster_cols = F. You need to make sure that the col order of your zscore is WT to SCA7