Creates a Heatmap using `TidyHeatmap` and `ComplexHeatmap`

plotTidyHeatmap(
  x,
  select_taxa = NULL,
  group_samples_by = NULL,
  add_taxa_label = TRUE,
  ...
)

Arguments

x: phyloseq-class object.
select_taxa: Features to plot.
group_samples_by: A column in sample_data to group tiles.
add_taxa_label: Logical. Default is TRUE.
...: Arguments forwarded to tidyHeatmap::heatmap and ComplexHeatmap::Heatmap.

Value

a heatmap object.

Details

A TidyHeatmap plotting wrapper for phyloseq-class object.

References

Shetty SA (2021). Data visualization for microbiome analytics. https://github.com/microsud/biomeViz

Author

Sudarshan A. Shetty

Examples

library(biomeUtils)
library(biomeViz)
library(microbiome)
library(dplyr)

ps <- FuentesIliGutData %>%
         microbiome::transform("compositional")
select_taxa <- findTopTaxa(ps, top= 10, method="mean")

plotTidyHeatmap(ps, select_taxa = select_taxa,
                group_samples_by = "ILI",
                add_taxa_label = FALSE,
                cluster_rows = FALSE,
                .scale = "none",
                transform = NULL,
                palette_value = c("red", "white", "blue"))
#> Registered S3 method overwritten by 'dendextend':
#>   method     from 
#>   rev.hclust vegan
#> tidyHeatmap says: (once per session) from release 1.7.0 the scaling is set to "none" by default. Please use scale = "row", "column" or "both" to apply scaling
#> Warning: The `.scale` argument of `heatmap()` is deprecated as of tidyHeatmap 1.7.0.
#> Please use scale (without dot prefix) instead: heatmap(scale = ...)
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.