ggbartax: taxonomy barplot

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

taxonomy barplot

Description

taxonomy barplot

Usage

ggbartax(obj, ...)

ggbartaxa(obj, ...)

## S3 method for class 'phyloseq'
ggbartax(obj, ...)

## S3 method for class 'data.frame'
ggbartax(
  obj,
  mapping = NULL,
  position = "stack",
  stat = "identity",
  width = 0.7,
  topn = 30,
  count = FALSE,
  sampleda = NULL,
  factorLevels = NULL,
  sampleLevels = NULL,
  facetNames = NULL,
  plotgroup = FALSE,
  groupfun = mean,
  ...
)

Arguments

obj	phyloseq, phyloseq class or data.frame, (nrow sample * ncol feature (factor)) or the data.frame for geom_bar.
...	additional parameters, see ggplot
mapping	set of aesthetic mapping of ggplot2, default is NULL, if the data is the data.frame for geom_bar, the mapping should be set.
position	character, default is 'stack'.
stat	character, default is 'identity'.
width	numeric, the width of bar, default is 0.7.
topn	integer, the top number of abundance taxonomy(feature).
count	logical, whether show the relative abundance.
sampleda	data.frame, (nrow sample * ncol factor), the sample information, if the data doesn't contain the information.
factorLevels	vector or list, the levels of the factors (contained names e.g. list(group=c("B","A","C")) or c(group=c("B","A","C"))), adjust the order of facet, default is NULL, if you want to order the levels of factor, you can set this.
sampleLevels	vector, adjust the order of x axis e.g. c("sample2", "sample4", "sample3"), default is NULL.
facetNames	character, default is NULL.
plotgroup	logical, whether calculate the mean or median etc for each group, default is FALSE.
groupfun	character, how to calculate for feature in each group, the default is 'mean', this will plot the mean of feature in each group.

Value

barplot of tax

Author(s)

Shuangbin Xu

Examples

## Not run: 
    library(ggplot2)
    data(test_otu_data)
    test_otu_data %<>% as.phyloseq()
    otubar <- ggbartax(test_otu_data) + 
              xlab(NULL) + ylab("relative abundance(%)")

## End(Not run)

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.