User specifed OTUs are plotted.
plot_select_taxa(
x,
select.taxa,
variableA,
palette,
plot.type,
group.order = NULL
)
phyloseq-class
object.
a character list of taxa to be plotted. eg. select.taxa <- c("OTU-370251", "OTU-311173", "OTU-341024").
Variable of interested to be checked. This will also be used to color the plot.
Any of the RColorBrewer plettes.
Three optons c("stripchart", "boxplot", "violin")
Default is NULL. a list specifing order of x-axis. E.g. c("H","CRC","nonCRC")
ggplot
object. This can be further modified using ggpubr.
Useful for instances where user is interested only in some OTUs. For example OTUs reported to be significantly diferent.
if (FALSE) {
# Example data
library(microbiome)
library(microbiomeutilities)
data("zackular2014")
p0 <- zackular2014
p0.f <- format_to_besthit(p0)
select.taxa <- c("OTU-d__denovo31:Dorea", "OTU-d__denovo24:Blautia")
p <- plot_select_taxa(p0.f, select.taxa, "DiseaseState", "Paired", plot.type = "stripchart")
print(p)
}