humann2Barplot: humann2Barplot

In philippmuench/PMtools: Miscellaneous helper functions

Description

Generates barplots statified by taxon and metadata for one HUMAnN2 feature, similar to 'humann2_barplot' Optimized for viewability of many features in one figure by limiting the number of statifications.

Usage

humann2Barplot(
  humann2.table,
  num.bugs = "auto",
  num.bugs.explained.fraction = 0.25,
  feature = "Cas1",
  featue.column = 1,
  taxa.column = 2,
  metadata,
  metadata.id = 9,
  metadata.factor = 4,
  use.custom.column.stratification = T,
  order.by = "bc",
  column.stratification.order = c("Oral", "Skin", "Vaginal", "Gut"),
  custom.order,
  last.plot.colors = NULL
)

Arguments

humann2.table	a dataframe containing the HUMAnN2 output in tsv format
num.bugs	number of most abundant bugs to show as statification, set to to "auto" if this should be ajusted based on num.bugs.explained.fraction
num.bugs.explained.fraction	fraction that needs to be explained by the number of bugs shown
feature	name of gene in humann2_table that will be plotted
featue.column	index of column in humann2 table that holds the feature
taxa.column	index of column in humann2 table that holds the taxon infomation
metadata	a dataframe containing the metadata
metadata.id	column in metadata file that holds the smaple id (colum names in humann2 table)
metadata.factor	column in metadata file that holds the annotation of interest
use.custom.column.stratification	custom orderin of row statification
order.by	how to order bars within one statification
column.stratification.order	oder of entries in metadata.factor
custom.order	custom sample order
last.plot.colors	dataframe of plot colors for additional cross-lookup of taxa information

philippmuench/PMtools documentation built on Dec. 27, 2019, 8:08 a.m.