hotplot | R Documentation |
Coloured bimodality plot.
hotplot(
x,
taxon,
tipping.point = NULL,
lims = NULL,
shift = 0.001,
log10 = TRUE
)
x |
|
taxon |
Taxonomic group to visualize. |
tipping.point |
Indicate critical point for abundance variations to be highlighted. |
lims |
Optional. Figure X axis limits. |
shift |
Small constant to avoid problems with zeroes in log10 |
log10 |
Use log10 abundances for the OTU table and tipping point |
ggplot
object
Contact: Leo Lahti microbiome-admin@googlegroups.com
See citation('microbiome')
data(atlas1006)
pseq <- subset_samples(atlas1006, DNA_extraction_method == 'r')
pseq <- transform(pseq, 'compositional')
# Set a tipping point manually
tipp <- .3/100 # .3 percent relative abundance
# Bimodality is often best visible at log10 relative abundances
p <- hotplot(pseq, 'Dialister', tipping.point=tipp, log10=TRUE)
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