ggbartax {MicrobiotaProcess} | R Documentation |
taxonomy barplot
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, ... )
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 |
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. |
barplot of tax
Shuangbin Xu
## 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)