Italicise annotations with pheatmap

Question

[jamie.pike]

Hello,

I have some column annotations in a heatmap (generated with pheatmap), which correspond to species that i want to be in italics.

I have read through the pheatmap documentation and I can't find anything. I have also tried to find and adapt solutions online (for example), but most tutorials and posts refer to italicising the row or column names, not the annotations in the legend. I have tried to apply some of these techniques to my script but with no luck.

Is anyone able to suggest a solution? I have seen lots of posts about complex heatmaps, but from what I can work out it is not so easy to do with that either. Surely having species or genes in the annotations, which should technically be italicised, is common?

---

Here is what I have so far:

#Create a list containing the colours we want to use for the annotations. 
ann_colours = list(
  Race= c("Race 1" = "orange2", "Race 4" = "blue"),
  "Forma_specialis" = c("apii" = "lightskyblue", "cepae" = "purple", "conglutinans" = "orange", "coriandrii" = "pink", "cubense" = "khaki1", "lactucae" = "green3", "lini" = "indianred", "lycopersici" = "red", "matthiolae" = "blue", "narcissus" = "yellow", "niveum" = "brown", "rapae" = "dark green", "rocket" = "light green", "vasinfectum" = "greenyellow", "non-pathogenic" = "black"), 

newnames_rows <- lapply(
  colnames(HeatmapData_Binary),
  function(x) bquote(italic(.(x)))) #This works perfectly for the rows of course - but it's not what I need!

#Try to apply to the annotations
newnames <- lapply(
  list(ann_colours),
  function(x) bquote(italic(.(x)))) 

If I print newnames:

italic(list(Race = c(`Race 1` = "orange2", `Race 4` = "blue"), 
    Forma_specialis = c(apii = "lightskyblue", cepae = "purple", 
    conglutinans = "orange", coriandrii = "pink", cubense = "khaki1", 
    lactucae = "green3", lini = "indianred", lycopersici = "red", 
    matthiolae = "blue", narcissus = "yellow", niveum = "brown", 
    rapae = "dark green", rocket = "light green", vasinfectum = "greenyellow", 
    `non-pathogenic` = "black"), Lactucae_Distribution = c(`Race 1 Specific` = "tan1", 
    `Race 4 Specific` = "skyblue3", Shared = "green", `Not Race Specific` = "grey"
    ))) 

I imagine the issue is because I am not trying to italicise the information in the df, but instead the 'ann_colours' list?

Here is my pheatmap script:

HeatmapData_Binary %>%
  pheatmap(color = colorRampPalette(c("grey90", "firebrick"))(2),
           legend = T,
           legend_breaks = c(0.75, 0.25),
           legend_labels = c("Present", "Absent"),
           drop_levels = F,
           cluster_rows = CEC_Clustering,
           cluster_cols = Fsp_Clustering,
           cellheight = 5.5,
           cellwidth = 60,
           annotation_row = RowAnnotations,
           annotation_col = ColAnnotations,
           annotation_colors = newnames,
           fontsize_row = 2.5,
           fontsize = 24,
           treeheight_row = 10,
           angle_col = 90,
           cutree_cols = 14,
           show_rownames = F,
           na_col = "white",
           border_color = "grey90",
           labels_col = Isolist,
           filename = "./FolaEffectorsHeatmap-Draft1.pdf",
           height = 30,
           width = 25)

Pheatmap which does not contain italicised annotations:

I am so close to having this figure finished! This has been plaguing me for days! Please help!

Thank you, Jamie!

[ATpoint]

I might be the party pooper but I generally think that these sorts of aesthetics should be done later in something like Inkscape. In R do the figure, in appropriate dimensions and font size and then do everything to make it look publication-ready later. No need to waste time trying to code up everything in R. You're producing dozens or hundreds of plots during a project, and only a few percent will make the paper, not worth losing too much time doing the beauty work on plots that will never again see any daylight.

[jamie.pike]

@ATpoint Very true! I'm not so familiar with many image editing software and I wonder if it will be just as quick for me to try in R, but I think for some of the stuff I want to achieve with this figure that will be the best bet! Thank you (:

[ATpoint]

Inkscape you learn in a day, for basic image and figure manipulation it's really simple and a good skill to have. Highly recommended.

Answer 1

[swbarnes2]

You might not want to hear this...but you can probably do it with ComplexHeatMap. I put superscripts in ComplexHeatmap, so you should be able to do italics.

[Trivas]

Just want to add that ComplexHeatMap > pheatmap for most things and it's very easy to port code over.

From version 2.5.2 of ComplexHeatmap, I implemented a new ComplexHeatmap::pheatmap() function which actually maps all the parameters in pheatmap::pheatmap() to proper parameters in ComplexHeatmap::Heatmap(), which means, it converts a pheatmap to a complex heatmap.

[jamie.pike]

You're right, I was trying to save time and not write for in ComplexHeatmap, but using @Trivas ComplexHeatmap::pheatmap() should help! Thank you both (: