View source: R/abundance_heatmap.R
abundance_heatmap | R Documentation |
Takes a phyloseq-class
object as input and
creates a ggplot-heatmap of the abundances across samples.
The default color choice is the viridis palette, which is supposed to
be both aesthetic for normal and color-blind viewers.
abundance_heatmap(phyloseq_obj, treatment, subset = NULL,
classification = NULL, transformation = 'none', colors = 'default',
treatment_labels = NULL, sample_labels = NULL, classification_labels= NULL)
phyloseq_obj |
A |
treatment |
Column name as a string or number in the
|
subset |
A factor within the |
classification |
Column name as a string or number in the
|
transformation |
Transformation to be used on the data. "none", "relative_abundance", "log", "log10", "log1p", "log2", "asn", "atanh", "boxcox", "exp", "identity", "logit", "probability", "probit", "reciprocal", "reverse" and "sqrt" |
colors |
Name of a color set from the RColorBrewer package or a vector palette of R-accepted colors. |
treatment_labels |
a vector of names to be used as labels for treatments/facets. |
sample_labels |
a vector of names to be used as labels for Samples. |
classification_labels |
a vector of names to be used as labels for the taxonomic classifications. |
ggplot-object
abundance_heatmap(soil_column, classification = 'Phylum',
treatment = c('Matrix', 'Treatment'), transformation = 'log')
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