HI All,
I'm fairly in new with R, so any help is much appreciated. I'm in the process of making a heatmap using the pheatmap function. I'm adding a column color bar so that I can associate specific data in the header with specific colors in the color bar. So for example I want anything that contains the number 1 in the header of my entire data set to be labeled as Male and have a specific color associated with it in the column color bar.
I'm using the following code as an example to try to do this:
require(pheatmap)
# dummy data
dummymat = matrix(rnorm(100), 10, 10)
colnames(dummymat) = paste("Patient", 1:10, sep = "")
rownames(dummymat) = paste("Gene", 1:10, sep = "")
# create a data frame with the patients categories
categories
Dear Afshin,
I would propose to switch to the Bioconductor package ComplexHeatmap; see http://www.bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html
There are a lot of examples in the documentation; e.g. adding annotations is explained in
http://www.bioconductor.org/packages/release/bioc/vignettes/ComplexHeatmap/inst/doc/s4.heatmap_annotation.html
Best,
Matthias
Dear Afshin,
I would propose to switch to the Bioconductor package ComplexHeatmap; see http://www.bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html
There are a lot of examples in the documentation; e.g. adding annotations is explained in
http://www.bioconductor.org/packages/release/bioc/vignettes/ComplexHeatmap/inst/doc/s4.heatmap_annotation.html
Best,
Matthias
Hi Matthias,
I will take a look. I was hoping there might be an easy solution... I'm sure there is.. For now I will take a look at the package you recommended.
Thanks
Afshin
The problem with all the examples for this, is that it never shows how to specifically associate or gives any information on the example I have above with header in the data. All there examples for the color bar are specifically setting certain samples to certain colors. For example they set samples 1 - 5 to be called "a" and color that red. So not sure how to actually do what I want to do based on these examples (unless I'm missing something). Do you have any other suggestions? Thanks.
Check out the `colormap()`, `imagep()`, and `drawPalette()` functions in the oce package.
Please take a look at these codes. I used 'aheatmap' function from library(NMF) instead library(pheatmap).
Is this what you want? The heatmap is attached.
You can also eliminate the dendrogram by replacing Colv=TRUE, Rowv=TRUE with Colv=NA, Rowv=NA when run the plot.
set.seed(1818)
library(NMF)
library(gplots)
dummymat = matrix(rnorm(100), 10, 10)
colnames(dummymat) = paste("Patient", 1:10, sep = "")
rownames(dummymat) = paste("Gene", 1:10, sep = "")
categories
The easy way is to use a colormap arealy build. Mat Lab has a color map designed for such proposes-
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