Change fontsize/remove name of annotation ComplexHeatmap package
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camillab. ▴ 10
@camillab-23642
Last seen 6 months ago
London

Hi,

How do I remove the label that is next to the annotation box in the heatmap with ComplexHeatmap ideally I would like to create a block annotation with the name of the sample in it but so far I wasn't able to do it. Also which RGB color is the best to have blue and red and not purple-bluish color in the heatmap? I have 3 samples (ctrl) and 3 treatments. I want the samples in columns and the genes in rows. here my code:

#load libraries 
library(grid) 
library("ComplexHeatmap")
library(circlize)

#set color heatmap 
colr = colorRamp2(
        seq(min(mydata), max(mydata), length = 3),
        c("#000099", "#EEEEEE", "#FF0000"),
        space = "RGB")

# annotation 
df = data.frame(sample = c(rep("CTRL", 3), rep("GENT", 3))) 
ha = HeatmapAnnotation(
            df = df, 
            col = list(sample = c("CTRL" ="black", "TREAT" = "yellow")),
            simple_anno_size = unit(2, "mm")
            )

a <- Heatmap(t(mydata),
             name = "z score", #title of legend
             width = unit(8, "cm"), height = unit(8, "cm"),
             show_column_names = FALSE,
             column_title = " ", 
             row_title = "Genes",
             col= colr,
             border = TRUE,
             column_names_gp = grid::gpar(fontsize = 9),
             column_title_gp = gpar(fontsize = 11),
             row_title_gp = gpar(fontsize = 11),
             clustering_distance_rows= "euclidean",
             clustering_distance_columns=  "euclidean",
             clustering_method_rows = "ward.D2" ,
             clustering_method_columns="ward.D2",
             row_dend_side = "left",
             top_annotation = ha)

        draw(a, merge_legend = TRUE) # join the two legends

thank you!

r rnaseq complexHeatmap annotation • 1.4k views
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Was originally posted on Biostars: https://www.biostars.org/p/443858/

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Zuguang Gu ▴ 210
@zuguang-gu-7797
Last seen 1 day ago
Germany / Heidelberg / DKFZ
  1. set showannotationname to FALSE

  2. You don't need to use block annotation. You can first set showcolumnnames =FALSE and then add a column annotation with annotext() with setting background colors. See the last plot in https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#text-annotation The gpar in annotext() maybe can also be set with columnnamesgp argument in Heatmap(), but I haven't tried.

  3. Can you just use blue-white-red colors? This is the default color pattern in ComplexHeatmap.

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thank you!! I have another problem now, I cannot export in tiff/png (high resolution) the heatmap generate! I don't understand why! i have no problem with the pdf version but when I try with png or tiff I have problem!

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Can you elaborate on what is the problem?; and also provide any status, warning, or error messages? - thank you.

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I sorted it out! it was setting up the wrong dimension size for the image to be exported (width/height)!

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Wonderful - thanks.

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