ggbartax {MicrobiotaProcess} | R Documentation |
taxonomy barplot
ggbartax(obj, ...) ## S3 method for class 'phyloseq' ggbartax(obj, ...) ## Default S3 method: ggbartax( obj, mapping = NULL, position = "stack", stat = "identity", width = 0.7, topn = 30, count = FALSE, sampleda = NULL, factorLevels = NULL, facetNames = NULL, plotgroup = FALSE, groupfun = mean, ... )
obj |
phyloseq, phyloseq class or data.frame, (nrow sample * ncol feature (factor)) or the data.frame for geom_bar. |
... |
additional parameters, see |
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 |
list, the levels of the factors, default is NULL, if you want to order the levels of factor, you can set this. |
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. |
barplot of tax
Shuangbin Xu
library(ggplot2) data(test_otu_data) otubar <- ggbartax(test_otu_data) + xlab(NULL) + ylab("relative abundance(%)")