hotplot {microbiome} | 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)