如何在heatmap.2中创建预注释的行侧列 [英] How to create pre-annotated rowside column in heatmap.2
本文介绍了如何在heatmap.2中创建预注释的行侧列的处理方法,对大家解决问题具有一定的参考价值,需要的朋友们下面随着小编来一起学习吧!
问题描述
我有以下数据:
dat <- structure(list(GO = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 3L, 3L, 3L, 4L, 5L, 5L, 5L, 5L, 5L, 5L), .Label = c("apoptotic process",
"metabolic process", "negative regulation of apoptotic process",
"positive regulation of apoptotic process", "signal transduction"
), class = "factor"), ProbeGene = structure(c(14L, 15L, 2L, 12L,
7L, 11L, 16L, 8L, 19L, 13L, 3L, 1L, 18L, 4L, 10L, 5L, 9L, 17L,
20L, 6L), .Label = c("1416787_at Acvr1", "1418835_at Phlda1",
"1419282_at Ccl12", "1423240_at Src", "1424896_at Gpr85", "1434186_at Lpar4",
"1434670_at Kif5a", "1440374_at Pde1c", "1440681_at Chrna7",
"1440803_x_at Tacr3", "1442017_at LOC101056574", "1448815_at Ogg1",
"1448821_at Tyr", "1451338_at Nisch", "1454721_at Arel1", "1456300_at Ilvbl",
"1456989_at Oxgr1", "1457580_at Chd8", "1457827_at Arsj", "1460657_at Wnt10a"
), class = "factor"), foo = c(1.412475312, 1.413647397, 1.41297239,
-0.707106781, -0.707106781, -0.707106781, -0.707106781, -0.707106781,
-0.707106781, -0.707106781, -0.707106781, -0.707106781, -0.707106781,
-0.707106781, -0.707106781, -0.707106781, -0.707106781, -0.707106781,
-0.707106781, -0.707106781), bar = c(-0.645532476, -0.741475951,
-0.655185417, -0.707106781, -0.707106781, -0.707106781, -0.707106781,
-0.707106781, -0.707106781, -0.707106781, -0.707106781, -0.707106781,
-0.707106781, -0.707106781, -0.707106781, -0.707106781, -0.707106781,
-0.707106781, -0.707106781, -0.707106781), aux = c(-0.766942837,
-0.672171445, -0.757786973, 1.414213562, 1.414213562, 1.414213562,
1.414213562, 1.414213562, 1.414213562, 1.414213562, 1.414213562,
1.414213562, 1.414213562, 1.414213562, 1.414213562, 1.414213562,
1.414213562, 1.414213562, 1.414213562, 1.414213562)), .Names = c("GO",
"ProbeGene", "foo", "bar", "aux"), row.names = c(50L, 35L, 45L,
74L, 61L, 101L, 96L, 68L, 69L, 75L, 113L, 127L, 109L, 135L, 150L,
152L, 183L, 190L, 197L, 191L), class = "data.frame")
它看起来像这样(它们按GO
列排序):
It looks like this (they are sorted by GO
column):
> dat
GO ProbeGene foo bar aux
50 apoptotic process 1451338_at Nisch 1.4124753 -0.6455325 -0.7669428
35 apoptotic process 1454721_at Arel1 1.4136474 -0.7414760 -0.6721714
45 apoptotic process 1418835_at Phlda1 1.4129724 -0.6551854 -0.7577870
74 metabolic process 1448815_at Ogg1 -0.7071068 -0.7071068 1.4142136
61 metabolic process 1434670_at Kif5a -0.7071068 -0.7071068 1.4142136
101 metabolic process 1442017_at LOC101056574 -0.7071068 -0.7071068 1.4142136
96 metabolic process 1456300_at Ilvbl -0.7071068 -0.7071068 1.4142136
68 metabolic process 1440374_at Pde1c -0.7071068 -0.7071068 1.4142136
69 metabolic process 1457827_at Arsj -0.7071068 -0.7071068 1.4142136
75 metabolic process 1448821_at Tyr -0.7071068 -0.7071068 1.4142136
113 negative regulation of apoptotic process 1419282_at Ccl12 -0.7071068 -0.7071068 1.4142136
127 negative regulation of apoptotic process 1416787_at Acvr1 -0.7071068 -0.7071068 1.4142136
109 negative regulation of apoptotic process 1457580_at Chd8 -0.7071068 -0.7071068 1.4142136
135 positive regulation of apoptotic process 1423240_at Src -0.7071068 -0.7071068 1.4142136
150 signal transduction 1440803_x_at Tacr3 -0.7071068 -0.7071068 1.4142136
152 signal transduction 1424896_at Gpr85 -0.7071068 -0.7071068 1.4142136
183 signal transduction 1440681_at Chrna7 -0.7071068 -0.7071068 1.4142136
190 signal transduction 1456989_at Oxgr1 -0.7071068 -0.7071068 1.4142136
197 signal transduction 1460657_at Wnt10a -0.7071068 -0.7071068 1.4142136
191 signal transduction 1434186_at Lpar4 -0.7071068 -0.7071068 1.4142136
>
我想做的是创建一个带有行侧颜色的热图,以表示GO
列.最后,它看起来像这样(我手动添加了蓝色列):
What I want to do is to create a heatmap with row side color that denote the GO
columns. In the end it will look like this (I manually add the blue column):
我坚持下面的代码:
library(gplots)
dat.tmp <- dat
dat.tmp$GO <- NULL
rownames(dat.tmp) <- dat.tmp$ProbeGene
dat.tmp$ProbeGene <- NULL
heatmap.2(as.matrix(dat.tmp),margin=c(5,15),dendrogram="none",trace="none",scale="row")
推荐答案
这是一种方法,尽管它与您所拥有的不完全相同:
This would be one approach, though it's not exactly like what you have:
# Note the Rowv=TRUE argument to prevent reordering of rows
heatmap.2(as.matrix(dat.tmp),margin=c(5,15),dendrogram="none",trace="none",scale="row",
Rowv=FALSE, RowSideColors=as.character(as.numeric(dat$GO)))
legend("topright",
legend = unique(dat$GO),
col = unique(as.numeric(dat$GO)),
lty= 1,
lwd = 5,
cex=.7
)
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