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 <- data.frame(Sex = factor(sample(c("1", "2"),size = 10,replace = T), labels = c("Male", "Female")), Stage= factor(sample(c('Patient10','Patient9','patient5'),size = 10,replace = T), labels = c('I','II','III')))
rownames(categories) <- colnames(dummymat)
pheatmap(dummymat, color = colorRampPalette(c("navy", "white", "firebrick3"))(50), clustering_method = "mcquitty",
clustering_distance_rows = "euclidean", clustering_distance_cols = "euclidean",
scale = 'none', annotation = categories)
Obviously from the above code I don't get what I want. I'm sure I using the wrong functions here to do this (since I'm a beginner in R)
Can anyone help with my question? I would really appreciate any input and help that anyone can give.
Thanks,
Afshin
