Question: Retrieve Clusters From ComplexHeatmap
0
pthom010 • 0 wrote:
I made a heatmap with the following data (the actual table has 240 rows):
tf.log
0-dpi 1-dpi 7-dpi 14-dpi 22-dpi
TRINITY_DN0_c0_g1_i2 1.27584408 0.5872404 1.780178 1.414362 1.53341851
TRINITY_DN10214_c0_g1_i2 -2.34774378 -2.9194079 -3.211677 -2.885869 -2.04617227
TRINITY_DN10214_c0_g1_i6 -2.14867876 -1.5794957 -1.577811 -2.485095 -1.44172768
TRINITY_DN1038_c0_g1_i4 0.03163921 0.7375222 2.037936 2.462830 0.04559793
TRINITY_DN10462_c0_g1_i2 -2.63973533 -2.8039350 -2.481144 -2.698932 -1.76284020
TRINITY_DN1052_c0_g1_i3 -3.32767605 -2.2006082 -1.887869 -1.211592 -1.43292669
I then made the following heatmap:
heat.gen.k = Heatmap(tf.log, width = unit(10, "cm"),
km = 12,
cluster_columns = F,
show_row_names = F,
row_title_rot = 0,
row_gap = unit(3, "mm"),
name = "Log2FC",
column_title = "Resistant - Susceptible",
column_title_gp = gpar(fontfamily = "sans", fontsize = 28),
column_names_gp = gpar(fontfamily = "sans", fontsize = 20),
col = heat.col,
right_annotation = ha)
print(heat.gen.k)
I would like to pull the clusters out for downstream analysis but I cannot do so with the following code:
clusterlist = row_order(heat.gen.k)
clu_df <- lapply(names(clusterlist), function(i){
out <- data.frame(GeneID = rownames(tf.log[clusterlist[[i]],]),
Cluster = paste0("cluster", i),
stringsAsFactors = FALSE)
return(out)
}) %>%
do.call(rbind, .)
I keep getting the following error:
Error in data.frame(GeneID = rownames(tf.log[clusterlist[[i]], ]), Cluster = paste0("cluster", :
arguments imply differing number of rows: 0, 1
Not sure how to resolve this issue.
