我知道如何使用 pheatmap 按注释类别对行（基因）进行分组，并且我知道如何对整个行（基因）集执行 Person 的相关聚类，但我想要完成的是执行聚类（并显示独立的树状图）独立于每个类别。
这甚至可能吗？或者我是否被迫为每个类别创建单独的热图以在类别的基础上进行聚类？
在下面检查我的 MWE：
set.seed(1)
library(pheatmap)
mymat <- matrix(rexp(600, rate=.1), ncol=12)
colnames(mymat) <- c(rep("treatment_1", 3), rep("treatment_2", 3), rep("treatment_3", 3), rep("treatment_4", 3))
rownames(mymat) <- paste("gene", 1:dim(mymat)[1], sep="_")
annotdf <- data.frame(row.names = paste("gene", 1:dim(mymat)[1], sep="_"), category = c(rep("CATEGORY_1", 10), rep("CATEGORY_2", 10), rep("CATEGORY_3", 10), rep("CATEGORY_4", 10), rep("CATEGORY_5", 10)))
pheatmap(mymat,
scale="row",
cluster_rows = FALSE,
cluster_cols = FALSE,
gaps_row=c(10,20,30,40),
gaps_col=c(3,6,9),
cellheight = 6,
cellwidth = 20,
border_color=NA,
fontsize_row = 6,
filename = "TEST1.png",
annotation_row = annotdf
)
pheatmap(mymat,
scale="row",
cluster_rows = …我有以下 MWE，我在其中制作了一个热图，而没有执行任何聚类和显示任何树状图。我想以比现在更好看的方式将我的行（基因）按类别分组在一起。
这是 MWE：
#MWE
library(gplots)
mymat <- matrix(rexp(600, rate=.1), ncol=12)
colnames(mymat) <- c(rep("treatment_1", 3), rep("treatment_2", 3), rep("treatment_3", 3), rep("treatment_4", 3))
rownames(mymat) <- paste("gene", 1:dim(mymat)[1], sep="_")
rownames(mymat) <- paste(rownames(mymat), c(rep("CATEGORY_1", 10), rep("CATEGORY_2", 10), rep("CATEGORY_3", 10), rep("CATEGORY_4", 10), rep("CATEGORY_5", 10)), sep=" --- ")
mymat #50x12 MATRIX. 50 GENES IN 5 CATEGORIES, ACROSS 4 TREATMENTS WITH 3 REPLICATES EACH
png(filename="TEST.png", height=800, width=600)
print(
heatmap.2(mymat, col=greenred(75),
trace="none",
keysize=1,
margins=c(8,14),
scale="row",
dendrogram="none",
Colv = FALSE,
Rowv = FALSE,
cexRow=0.5 + 1/log10(dim(mymat)[1]),
cexCol=1.25,
main="Genes grouped …