plotAbundance: Plotting abundance data

In microbiome/miaViz: Microbiome Analysis Plotting and Visualization

Plotting abundance data

Description

plotAbundance plots the abundance on a selected taxonomic rank. Since this probably makes sense only for relative abundance data, the assay used by default is expected to be in the slot ‘relabundance’. If only ‘counts’ is present, the relative abundance is computed.

Usage

plotAbundance(x, ...)

## S4 method for signature 'SummarizedExperiment'
plotAbundance(
  x,
  rank = taxonomyRanks(x)[1],
  features = NULL,
  order_rank_by = c("name", "abund", "revabund"),
  order_sample_by = NULL,
  decreasing = TRUE,
  use_relative = TRUE,
  layout = c("bar", "point"),
  one_facet = TRUE,
  ncol = 2,
  scales = "fixed",
  assay.type = assay_name,
  assay_name = "counts",
  ...
)

Arguments

x	a SummarizedExperiment object.
...	additional parameters for plotting. See mia-plot-args for more details i.e. call help("mia-plot-args")
rank	a single character value defining the taxonomic rank to use. Must be a value of taxonomyRanks(x).
features	a single character value defining a column from colData to be plotted below the abundance plot. Continuous numeric values will be plotted as point, whereas factors and character will be plotted as colour-code bar. (default: features = NULL)
order_rank_by	How to order abundance value: By name (“name”) for sorting the taxonomic labels alphabetically, by abundance (“abund”) to sort by abundance values or by a reverse order of abundance values (“revabund”).
order_sample_by	A single character value from the chosen rank of abundance data or from colData to select values to order the abundance plot by. (default: order_sample_by = NULL)
decreasing	TRUE or FALSE: If the order_sample_by is defined and the values are numeric, should the values used to order in decreasing or increasing fashion? (default: decreasing = FALSE)
use_relative	TRUE or FALSE: Should the relative values be calculated? (default: use_relative = TRUE)
layout	Either “bar” or “point”.
one_facet	Should the plot be returned in on facet or split into different facet, one facet per different value detect in rank. If features or order_sample_by is not NULL, this setting will be disregarded.
ncol, scales	if one_facet = FALSE, ncol defines many columns should be for plotting the different facets and scales is used to define the behavior of the scales of each facet. Both values are passed onto facet_wrap.
assay.type	a character value defining which assay data to use. (default: assay.type = "relabundance")
assay_name	a single character value for specifying which assay to use for calculation. (Please use assay.type instead. At some point assay_name will be disabled.)

Details

Subsetting to rows of interested and ordering of those is expected to be done outside of this functions, e.g. x[1:2,]. This will plot data of all features present.

Value

a ggplot object or list of two ggplot objects, if features are added to the plot.

Examples

data(GlobalPatterns, package="mia")
se <- GlobalPatterns

## Plotting abundance using the first taxonomic rank as default
plotAbundance(se, assay.type="counts")

## Using "Phylum" as rank
plotAbundance(se, assay.type="counts", rank = "Phylum", add_legend = FALSE)

## If rank is set to NULL plotAbundance behaves like plotExpression
plotAbundance(se, assay.type="counts", rank = NULL,
           features = head(rownames(se)))
  
## A feature from colData or taxon from chosen rank can be used for ordering samples.
plotAbundance(se, assay.type="counts", rank = "Phylum",
           order_sample_by = "Bacteroidetes")

## Features from colData can be plotted together with abundance plot.
# Returned object is a list that includes two plot; other visualizes abundance
# other features. 
plot <- plotAbundance(se, assay.type = "counts", rank = "Phylum",
                   features = "SampleType")

# These two plots can be combined with wrap_plots function from patchwork package
library(patchwork)
wrap_plots(plot, ncol = 1)


## Same plot as above but showing sample IDs as labels for the x axis on the top plot

plot[[1]] <- plotAbundance(se, assay.type = "counts", rank = "Phylum",
                           features = "SampleType", add_legend = FALSE,
                           add_x_text = TRUE)[[1]] +
                           theme(axis.text.x = element_text(angle = 90)) 

wrap_plots(plot, ncol = 1, heights = c(0.8,0.2))


## Compositional barplot with top 5 taxa and samples sorted by "Bacteroidetes"

# Getting top taxa on a Phylum level
se <- transformAssay(se, method="relabundance")
se_phylum <- agglomerateByRank(se, rank ="Phylum", onRankOnly=TRUE)
top_taxa <- getTopTaxa(se_phylum,top = 5, assay.type = "relabundance")

# Renaming the "Phylum" rank to keep only top taxa and the rest to "Other"
phylum_renamed <- lapply(rowData(se)$Phylum,
                       function(x){if (x %in% top_taxa) {x} else {"Other"}})
rowData(se)$Phylum <- as.character(phylum_renamed)

# Compositional barplot
plotAbundance(se, assay.type="relabundance", rank = "Phylum",
           order_rank_by="abund", order_sample_by = "Bacteroidetes")

microbiome/miaViz documentation built on Sept. 12, 2023, 8:02 a.m.