Heatmap error: heat_palette() palette argument must be either a: vector of colours, or....

[Leran10]

Hi,

I'm trying the example heatmap code on my study,

cols <- distinct_palette(n = 3, add = NA)
names(cols) <- unique(samdat_tbl(psq)$DiseaseState)

psq %>% 
  tax_transform("compositional", rank = "Class") %>% 
  comp_heatmap(
    tax_anno = taxAnnotation(
      Prev. = anno_tax_prev(bar_width = 0.3, size = grid::unit(1, "cm"))
    ),
    sample_anno = sampleAnnotation(
      State1 = anno_sample("DiseaseState"),
      col = list(State1 = cols), border = FALSE,
      State2 = anno_sample_cat("DiseaseState", col = cols)
    )
  ) 

But I kept getting error says:

Error: 
heat_palette() palette argument must be either a:
- vector of colours, or
- palette name from colorspace::hcl_palettes(type = 'diverging')
- palette name from colorspace::divergingx_palettes()
- palette name from colorspace::hcl_palettes(type = 'sequential')

After I added colors = heat_palette(sym = TRUE) after the "sampleAnnotation()" part in comp_heatmap(), the error is gone.

Is this line necessary here or did I misunderstood anything?

Thanks! Leran

[david-barnett]

Does the code run without errors when using the tutorial data?

Additionally, as a general approach, try simplifying the example code to help you (and me) figure out what is causing the error. e.g. does the following work on your dataset, or throw the same error? psq %>% tax_transform("compositional", rank = "Class") %>% comp_heatmap()