Description Usage Arguments Details Value Examples
View source: R/plot_select_taxa.R
User specifed OTUs are plotted.
1 | plot_select_taxa(x, select.taxa, variableA, palette, plot.type)
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x |
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select.taxa |
a character list of taxa to be plotted. eg. select.taxa <- c("OTU-370251", "OTU-311173", "OTU-341024", "OTU-179814"). |
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") |
Useful for instances where user is interested only in some OTUs. For example OTUs reported to be significantly diferent.
ggplot
object. This can be further modified using ggpubr.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## Not run:
# Example data
library(microbiome)
library(microbiomeUtilities)
data("biogeogut")
p0 <- biogeogut
select.taxa <- c("OTU-370251:Endozoicimonaceae", "OTU-311173:Helicobacteraceae")
p0.f <- format_to_besthit(p0)
p <- select_taxa_plot(ps2.f, select.taxa, "SampleType", "Paired", plot.type = "stripchart")
ggpar(p, yscale = "log10", ylab = "Abundance (log10)")
## End(Not run)
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