R摄影图: change annotation colors and prevent graphics window from popping up

在this question之后，我找到了pheatmap函数(与heatmap.2相比，它为我提供了对我想做的事情的更多控制)。

我有两个问题:

1-我无法更改注释(类别)的颜色

2-即使我将输出保存在png文件中，图形窗口也会不断弹出

这是我的MWE:

library(pheatmap)
library(RColorBrewer)
cols <- colorRampPalette(brewer.pal(9, "Set1"))

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)))

mycolors <- cols(length(unique(annotdf$category)))
names(mycolors) <- unique(annotdf$category)
mycolors <- list(mycolors = mycolors)

pheatmap(mymat,
     color=greenred(75),
     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,
     main="Genes grouped by categories",
     filename = "TEST.png",
     annotation_row = annotdf,
     annotation_colors = mycolors
)

产生:



正如您所看到的，这些颜色显然不是我指定的Set1调色板，而是默认的作弊贴图颜色(删除annotation_colors行将得到相同的结果)。



所以我的问题是:如何在Pheatmap中指定注解颜色？

另一方面，即使我将Pheatmap输出保存在png文件中，图形窗口也会不断弹出，如何防止这种情况发生？

谢谢!

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
 [1] LC_CTYPE=en_SG.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_SG.UTF-8        LC_COLLATE=en_SG.UTF-8
 [5] LC_MONETARY=en_SG.UTF-8    LC_MESSAGES=en_SG.UTF-8
 [7] LC_PAPER=en_SG.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_SG.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] gplots_3.0.1       RColorBrewer_1.1-2 pheatmap_1.0.8

loaded via a namespace (and not attached):
 [1] compiler_3.3.1     colorspace_1.2-6   scales_0.4.0       plyr_1.8.3
 [5] tools_3.3.1        gtable_0.2.0       Rcpp_0.12.7        KernSmooth_2.23-15
 [9] gdata_2.17.0       grid_3.3.1         caTools_1.17.1     bitops_1.0-6
[13] munsell_0.4.3      gtools_3.5.0

最佳答案

要为更多类别获得更多颜色，您将需要使用其他调色板。有许多连续的调色板，使您可以超越12个调色板(例如使用RColorBrewer)。

如果按原样在MWE中运行代码，则不应弹出R图形窗口。我运行了您的示例，并且在不打开控制台图形设备的情况下生成了所需的文件。如果您想比较以下是我的sessioInfo()。我会尝试关闭所有设备(graphics.off())，然后运行您的热图代码以查看是否可以解决问题。我还将检查以确保您在当前正在使用的目录中具有写权限？？？

正如@cuttlefish在其评论中所述，要获取自定义的行/颜色，以在颜色列表中显示名称，必须处理注释数据帧的colnames。

超过12种颜色

mymat <- matrix(rexp(720, 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 = rownames(mymat),
                      category = rep(paste0("Category_", seq(12)), each=5) )

newCols <- colorRampPalette(grDevices::rainbow(length(unique(annotdf$category))))
mycolors <- newCols(length(unique(annotdf$category)))
names(mycolors) <- unique(annotdf$category)
mycolors <- list(category = mycolors)

pheatmap(mymat,
         color=greenred(75),
         scale="row",
         cluster_rows = FALSE,
         cluster_cols = FALSE,
         gaps_row=c(5,10,15,20,25,30,35,40,45,50, 55),
         gaps_col=c(3,6,9),
         cellheight = 6,
         cellwidth = 20,
         border_color=NA,
         fontsize_row = 6,
         main="Genes grouped by categories",
         filename = "TEST_12cat.png",
         annotation_row = annotdf,
         annotation_colors = mycolors
)

session 信息

R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] pheatmap_1.0.8     RColorBrewer_1.1-2 gplots_3.0.1

loaded via a namespace (and not attached):
 [1] colorspace_1.3-0   scales_0.4.1       colorRamps_2.3     plyr_1.8.4         tools_3.3.0
 [6] gtable_0.2.0       Rcpp_0.12.7        KernSmooth_2.23-15 gdata_2.17.0       grid_3.3.0
[11] caTools_1.17.1     munsell_0.4.3      bitops_1.0-6       gtools_3.5.0