TaxaHeatmap: TaxaHeatmap

In zc1286/Wham: Workflow Hub for Automated Metagenomic Exploration (WHAM!)

Description

Visualization of Wham upstream analysis

Usage

TaxaHeatmap(
  object,
  taxa.level = c("k", "p", "o", "c", "f", "g", "s", "otu"),
  filter = c("all", "custom", "DE.filter"),
  custom,
  p.cutoff = 0.05,
  effect.size.range = c(0, 0),
  scale = T,
  col,
  column_split = F,
  annotation,
  count = c("rawCount", "WhamTransformation"),
  ...
)

Arguments

object	required. The output of WhamBiobakery, WhamEBI or Wham16s
taxa.level	Required, c("k","p","o","c","f","g","s").Collapse taxa at the provided level.
filter	c("all","custom","DE.filter"). Default is "all". "all" shows all samples. "custom" shows taxa provided by user and all samples. "DE.filter" shows taxa which pass DE test cutoff(p.cutoff and effect.size.range) and samples which are in the DE.result contrast.
custom	required when filter is set as "custom". A vector which contain taxa to be shown
p.cutoff	applied when filter is set as "DE.filter". Default is 0.05.
effect.size.range	applied when filter is set as "DE.filter" and aldex.module is set as t.test.Default range is c(0,0)
scale	default is TRUE. Z score is used when set as T. Expression counts are used when set as F
col	an argument in ComplexHeatmap::Heatmap: vector of colors if the color mapping is discrete or a color mapping function if the matrix is continuous numbers (should be generated by colorRamp2). If the matrix is continuous, the value can also be a vector of colors so that colors can be interpolated.
column_split	Split on columns.TRUE, FALSE or a vector provided by users.Default value is False. Column will be spilt based on annotation.
annotation	optional. Default is the last variable in design. A character vector indicates what column of metadata will be used for annotation bar
count	c("rawCount","WhamTransformation"). Default value is "rawCount". Setting as "rawCount" uses original count. Setting as WhamTransformation converts count to ratio(count divided by the total sum of each sample), and then times one million( x 1000,000)
...	arguments in ComplexHeatmap::Heatmap

Value

a heatmap of taxonomy

Examples

# see the vignette for more details

zc1286/Wham documentation built on May 14, 2021, 8 p.m.