Ordering average of gene expression in heat map

Question

I want to plot a heat map in header I have the average of gene expression validated in lab for each sample

dput(heat[1:5,1:5])

structure(c(3.05574677859363, -0.451189292623471, -0.398066832453666, 
-0.456927931251448, -0.393418432279742, -0.270234667496526, -0.451189292623471, 
-0.398066832453666, -0.456927931251448, -0.393418432279742, -0.270234667496526, 
-0.451189292623471, -0.398066832453666, -0.456927931251448, -0.393418432279742, 
-0.270234667496526, -0.451189292623471, -0.398066832453666, 2.0338091136055, 
-0.393418432279742, -0.270234667496526, 1.76078923919148, 1.96896026174603, 
1.97960246116808, -0.393418432279742), .Dim = c(5L, 5L), .Dimnames = list(
    c("hsa-miR-548b-5p", "hsa-miR-181c-5p", "hsa-miR-181d-5p", 
    "hsa-miR-125a-3p", "hsa-miR-4286"), c("30566-001", "30566-002", 
    "30566-003", "30566-004", "30566-005")))


dput(m[1:5,c(2,7)])

structure(list(HealthStatus = c("Healthy", "Healthy", "Healthy", 
"Healthy", "Healthy"), Average = c(108.915677, 103.148873, 40.3359607, 
88.4329528, 87.7756577)), row.names = c("30566-001", "30566-002", 
"30566-003", "30566-004", "30566-005"), class = "data.frame")


pheatmap(heat, cluster_rows=T, show_rownames=T,
         cluster_cols=FALSE, annotation_col=m[,c(2,7)],
         annotation_colors=annot_colors)

How I can order average in a descending way?

Answer 1

If you order your matrix/data.frame you can sort your columns by decreasing "Average", e.g.

library(pheatmap)

heat <- structure(c(3.05574677859363, -0.451189292623471, -0.398066832453666, 
                    -0.456927931251448, -0.393418432279742, -0.270234667496526, -0.451189292623471, 
                    -0.398066832453666, -0.456927931251448, -0.393418432279742, -0.270234667496526, 
                    -0.451189292623471, -0.398066832453666, -0.456927931251448, -0.393418432279742, 
                    -0.270234667496526, -0.451189292623471, -0.398066832453666, 2.0338091136055, 
                    -0.393418432279742, -0.270234667496526, 1.76078923919148, 1.96896026174603, 
                    1.97960246116808, -0.393418432279742), .Dim = c(5L, 5L), .Dimnames = list(
                      c("hsa-miR-548b-5p", "hsa-miR-181c-5p", "hsa-miR-181d-5p", 
                        "hsa-miR-125a-3p", "hsa-miR-4286"), c("30566-001", "30566-002", 
                                                              "30566-003", "30566-004", "30566-005")))

m <- structure(list(HealthStatus = c("Healthy", "Healthy", "Healthy", 
                                     "Healthy", "Healthy"), Average = c(108.915677, 103.148873, 40.3359607, 
                                                                        88.4329528, 87.7756577)), row.names = c("30566-001", "30566-002", 
                                                                                                                "30566-003", "30566-004", "30566-005"), class = "data.frame")

pheatmap(heat[,order(m[,"Average"], decreasing = TRUE)], 
         cluster_rows=TRUE, show_rownames=T,
         cluster_cols=FALSE, annotation_col=m)

^{Created on 2023-09-06 with reprex v2.0.2}