make_heat_map_from_physeq: Internal function to draw heatmap from a physeq object.

Description Usage Arguments Value

View source: R/heatmap.R

Description

Internal function to draw heatmap from a physeq object.

Usage

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make_heat_map_from_physeq(physeq, taxa_data = NULL, group, block = NULL,
  compare = NULL, max_abundance_for_color = NULL, log_transform = FALSE,
  border_color = "grey60", filename = NA, tax_labels = NULL,
  tax_order = NULL, show_rownames = TRUE, cellwidth = NA,
  cellheight = NA, gaps_col = NULL, gradient_steps, custom_palette = NULL)

Arguments

physeq

Phyloseq object

taxa_data

Taxa annotation to show.

group

Name of column in sample metadata to group samples on (1st layer).

block

Name of column in sample metadata to subgroup samples on (2nd layer).

compare

Vector of values in group column to compare (e.g., HFD vs Control).

max_abundance_for_color

Maximum abundance to use in the color scale of 50 levels. If null, the 99.5th percentile in the data is used. If maximum value in the data is higher than this, this will be level 49 and max will be level 50.

border_color

Border color for the heatmap cells.

filename

Name of file to save the heatmap figure.

tax_labels

Character vector of names to be shown for each taxon. If NULL, names in the physeq object will be used.

tax_order

Character vector of the original taxon names in the order you want them shown. If NULL, order in tax_labels will be used.

gradient_steps

The steps for the 5-phase 50-level gradient is drawn.

Value

pheatmap object.


TBrach/MicrobiomeX documentation built on April 19, 2018, 12:25 a.m.