View source: R/plot_taxa_boxplot.R
plot_taxa_boxplot | R Documentation |
Plot taxon abundance for samples.
plot_taxa_boxplot( x, taxonomic.level, top.otu, keep.other = FALSE, group, title, group.colors = NULL, group.order = NULL, add.violin = TRUE, violin.opacity = 0.25, box.opacity = 0.25, dot.opacity = 0.25, dot.size = 2 )
x |
|
taxonomic.level |
Merge the OTUs (for phyloseq object) into a higher taxonomic level. This has to be one from colnames(tax_table(x)). |
top.otu |
Top number of taxa to plot. |
keep.other |
TRUE or FALSE. Default is FALSE. This will not plot taxa group as Other |
group |
Specify main variable of interest. This should be one of the variables in sample_variables(x). |
title |
title for the plot |
group.colors |
Colors for plotting groups |
group.order |
Default is NULL. a list specifing order of x-axis. E.g. c("H","CRC","nonCRC") |
add.violin |
Loical. If half violoin to the added. Default=TRUE |
violin.opacity |
If add.violin=TRUE, opacity for violin. |
box.opacity |
For ggplot alpha to determine opacity for box |
dot.opacity |
For ggplot alpha to determine opacity for points |
dot.size |
For ggplot alpha to determine size for points |
A ggplot
plot object.
## Not run: # Example data library(microbiomeutilities) library(RColorBrewer) data("zackular2014") ps0 <- zackular2014 mycols <- c("brown3", "steelblue", "grey50") pn <- plot_taxa_boxplot(ps0, taxonomic.level = "Phylum", top.otu = 6, group = "DiseaseState", title = "Relative abudance plot", keep.other = FALSE, group.order = c("H", "CRC", "nonCRC"), group.colors = mycols ) print(pn + theme_biome_utils()) ## End(Not run)
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