User specifed OTUs are plotted.

plot_select_taxa(x, select.taxa, variableA, palette, plot.type)

Arguments

x

phyloseq-class object.

select.taxa

a character list of taxa to be plotted. eg. select.taxa <- c("OTU-370251", "OTU-311173", "OTU-341024").

variableA

Variable of interested to be checked. This will also be used to color the plot.

palette

Any of the RColorBrewer plettes.

plot.type

Three optons c("stripchart", "boxplot", "violin")

Value

ggplot object. This can be further modified using ggpubr.

Details

Useful for instances where user is interested only in some OTUs. For example OTUs reported to be significantly diferent.

Examples

# NOT RUN {
  # 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)


# }