draw_taxa_heatmap: Draw a heatmap of the OTU abundances in a phyloseq object.
In TBrach/MicrobiomeX: eXtended Functions for Microbiome Analysis and Visualization

Description Usage Arguments Value Examples

Draw a heatmap of the OTU abundances in a phyloseq object.

draw_taxa_heatmap(physeq, taxa_data, group, compare = NULL, block = NULL,
  max_abundance_for_color = NULL, log_transform = FALSE,
  border_color = "grey60", filename = NA, show_rownames = TRUE,
  gradient_steps = c(0.01, 0.1, 0.5, 1), cellwidth = NA, cellheight = NA,
  gaps_col = NULL, custom_palette = NULL)

`physeq`	Phyloseq object
`taxa_data`	Taxa annotation to show.
`group`	Name of column in sample metadata to group samples on (1st layer).
`compare`	Vector of values in `group` column to compare (e.g., HFD vs Control).
`block`	Name of column in sample metadata to subgroup samples on (2nd layer).
`max_abundance_for_color`	Maximum abundance to use in the color scale.
`log_transform`	boolean specifying if data should be log-transformed.
`border_color`	Border color for the heatmap cells.
`filename`	Name of file to save the heatmap figure.
`show_rownames`	boolean specifying if column names are be shown.
`cellwidth`	`cellwidth` argument to `pheatmap()`.
`cellheight`	`cellheight` argument to `pheatmap()`.
`gaps_col`	`gaps_col` argument to `pheatmap()`.
`custom_palette`	Custom palette list to use (see example).

ggplot object.

## Not run: 
# Assuming that the 'physeq' variable has the genera for taxa, this will draw a heatmap of
# only the 4 genera listed in 'taxa_data' with samples first grouped by Diet and
# then by Enterotype. It will annotate the taxa based on their Phylum. Heatmap cells will have
# "grey60" borders.
pal = list(Diet = "Set2", Enterotype = "Pastel1", Significance = "PuRd")
taxa_data = list(Bacteroides = "Bacteroidetes", Prevotella = "Bacteroidetes", Roseburia = "Firmicutes", Blautia = "Firmicutes")
names(taxa_data) = c("Phylum")
draw_taxa_heatmap(physeq, taxa_data, group = "Diet", block = "Enterotype", custom_palette = pal, filename = "heatmap.pdf")

# Heatmap without borders
draw_taxa_heatmap(physeq, taxa_data, ..., border_color = NULL)

# Heatmap with black borders
draw_taxa_heatmap(physeq, taxa_data, ..., border_color = "black")

## End(Not run)