Mark annotation

[dorinemerlat]

Hi, I have a little issue with the mark annotations. I can add them to my heatmap but I would like to use two different colors following the fact that the genes are known or not. To add them I used that :

annot = rowAnnotation(foo = anno_mark(
    at = c(1, 4, 8),
    labels =  c("ALDH1A1", "UPTR", "CCNO"),
    labels_gp = gpar(col = "black", fontsize = 10)))

To obtain two different colors for annotation I thought I would use the list() in the different fields (like for the other annotation types), but it didn't work (error : at should be numeric row index corresponding to the matrix) :

annot = rowAnnotation(foo = anno_mark(
    at = list(new = c(1), known = c(4,8)),
    labels = list(new = c("ALDH1A1"), known = c("UPTR", "CCNO")),
    labels_gp = list(new = gpar(col = "black", fontsize = 10), known = gpar(col = "black", fontsize = 10))))

Is there any other way to put the annotations in different colors ?

Thanks :)

[jokergoo]

You can set col as a vector in labels_gp`:

annot = rowAnnotation(foo = anno_mark(
    at = c(1, 4, 8),
    labels =  c("ALDH1A1", "UPTR", "CCNO"),
    labels_gp = gpar(col = c("black", "red", "red"), fontsize = 10)))

Heatmap(matrix(rnorm(100), 10)) + annot

[dorinemerlat]

thank you, it works perfectly !