R中热图的颜色 [英] Colors for heatmap in R
问题描述
我正在用R制作热图，但是对于R来说还是很陌生，我有一些疑问:
I'm making a heatmap in R, but being very new to R, I have some questions:
我的数据是一个由21列和89行组成的大矩阵，包含从0到16的数字.我希望以一种热图的方式将热图着色为从0(白色)到16(深红色-或该颜色的任何颜色)清酒).甚至可能更幻想，使用从0到< 10的调色板(以使具有10个"hits"以上的点获得相同的颜色).
My data is a big matrix 21 columns and 89 rows, containing numbers from 0 to 16. I would like to get the heatmap colored in a heatmappy way from 0 (white) to 16 (dark red - or any color for that sake). Or maybe even fancier, have a color palette going from 0 to <10 (so that the points having above 10 "hits" get the same color).
有人可以帮我吗?非常感谢！
Can anyone help me with this ? Thanks alot!
我的代码:
library(ggplot2)
library("RColorBrewer")
AS <- read.csv("L:/Pseudoalteromonas/Heatmap antismash/HM_phyl.csv", sep=";")
row.names(AS) <- AS$Strain
AS <- AS[,2:21]
## The colors you specify.
my_palette <- colorRampPalette(c("white", "yellow","orange", "red"))(n = 299)
AS_matrix <- data.matrix(AS)
AS_heatmap <- heatmap(AS_matrix, Rowv=NA, Colv=NA, col = my_palette, scale="row", margins=c(5,10))
我的数据如下:
tail(HM)
Sideophore Bacteriocin Aryl.polyene Nrps T1pks T2pks T3pks T1pks.Nrps Lantipeptide Terpene Hserlactone Transatpks
S4048 0 2 0 2 0 0 0 0 1 0 0 1
S3655 1 2 2 0 0 0 0 0 0 0 0 0
S4060 0 2 0 7 0 1 1 2 1 0 0 1
S2607 0 2 0 10 1 1 1 4 1 0 0 1
S4054 0 2 1 3 0 0 0 4 1 0 1 1
S4047 0 2 1 7 0 0 0 4 1 0 1 1
Butyrolactone Indole Thiopeptide Ladderane Pufa Resorcinol Otherks Other
S4048 0 0 0 0 0 0 0 0
S3655 0 0 0 0 0 1 0 0
S4060 0 1 0 0 0 0 0 2
S2607 0 1 0 0 0 0 0 2
S4054 0 1 0 1 0 0 0 0
S4047 0 1 0 1 0 0 0 2
推荐答案
您可以将数据保留为data.frame并使用ggplot2(自从您调用ggplot2以来，这就是您要的目的?)
You could keep the data as a data.frame and use ggplot2 (it looks like that is what you are intending since you called ggplot2?)
library(ggplot2)
library(RColorBrewer)
library(tidyverse)
set.seed(12343)
# create matrix with 21 columns and 89 rows
# with numbers between 0 - 16
AS <- runif(n= 1869, min = 0, max = 16) %>%
matrix(., nrow = 89)
colnames(AS) <- LETTERS[1:21]
AS <- as.data.frame(AS)
AS$train <- 1:89
AS <- gather(AS, A:U, key = "colname", value="value")
ggplot(AS, aes(x = colname, y=train)) + geom_tile(aes(fill = value),
colour = "white") +
scale_fill_distiller(palette = "Reds", limits = c(0,10), na.value = "#de2d26",
direction = 1, labels = c(0.0, 2.5, 5.0, 7.5, "> 10.0"))
因此，使用您的代码，也许像这样:
So using your code, maybe something like this:
library(ggplot2)
library(RColorBrewer)
library(tidyverse)
AS <- read.csv("L:/Pseudoalteromonas/Heatmap antismash/HM_phyl.csv", sep=";")
# assume "train" is the row indicator, so we will use
# gather with -train argument to gather all columns but "train"
AS <- gather(AS, -train, key = "colname", value="value")
ggplot(AS, aes(x = colname, y=train)) + geom_tile(aes(fill = value),
colour = "white") +
scale_fill_distiller(palette = "Reds", limits = c(0,10), na.value = "#de2d26",
direction = 1, labels = c(0.0, 2.5, 5.0, 7.5, "> 10.0"))
# na.values (values >10) take maximum red color in Reds colorbrewer
这篇关于R中热图的颜色的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！
