Bar plot of taxon composition with group support

Sort taxa by summed abundance across all samples and plot sorted taxon composition with a bar per sample

groupBarplot(
  abundances,
  groups = c(),
  aggregate = "none",
  taxon.color.map = NULL,
  group.color.map = NULL,
  topTaxa = 10,
  sortGroupwise = TRUE,
  sumGroupwise = FALSE,
  group.order = c(),
  hide.taxa = c(),
  randSampleNum = NA,
  summedTaxonColor = "#a9a9a9",
  extendTaxonColorMap = FALSE,
  legend = TRUE,
  legend.shift = 1,
  legend.hidegroups = FALSE,
  ...
)

Arguments

abundances	a matrix with taxa as rows and samples as columns
groups	group membership vector with as many entries as samples
aggregate	if groups are given, plot the aggregate across the group (or its selected samples if randSampleNum is true); possible values: none, median and mean
taxon.color.map	map of taxon-specific colors, should match row names; taxa not present in the color map will be colored in summedTaxonColor
group.color.map	map of group-specific colors, should match group names
topTaxa	number of top taxa to be plotted
sortGroupwise	if true, samples are sorted according to groups
sumGroupwise	if true, taxa are summed and sorted separately across samples within each group (if true, samples are always sorted group-wise)
group.order	if a vector with group names (one for each group) is given, group samples will be sorted in the order indicated; can also be used to only plot selected groups
hide.taxa	do not consider these taxa as top-abundant taxa, but keep them among Others
randSampleNum	if larger 0, sortGroupwise is set to true and the indicated sample number is randomly selected for each group
summedTaxonColor	the color of the summed taxa, by default gray
extendTaxonColorMap	if true, taxa not in the taxon color map are added there and the extended color map is returned
legend	add a legend with the color code
legend.shift	increase/decrease this parameter to shift the color legend further to the right/left
legend.hidegroups	do not show the group memberships in the legend
\dots	Additional arguments passed to plot()

Value

if extendTaxonColorMap is true, the taxon color map is returned

Details

Note that taxa are always summed across all samples, also in the presence of a group membership vector, unless sumGroupwise is true.

Examples

data(ibd_taxa)
data(ibd_metadata)
groups=as.vector(ibd_metadata$Diagnosis)
# taxon abundances were prefiltered and therefore do not add up to 1
groupBarplot(ibd_taxa,groups=groups,randSampleNum=10)
#> [1] "Number of samples in group CD : 68"
#> [1] "Number of samples in group UC : 53"
#> [1] "Number of samples in group Control : 34"
# sum taxa group-wise for sorting instead across all samples
groupBarplot(ibd_taxa,groups=groups,sumGroupwise=TRUE, legend.hidegroups=TRUE)
#> [1] "Number of samples in group CD : 68"
#> [1] "Number of samples in group UC : 53"
#> [1] "Number of samples in group Control : 34"
data(ibd_lineages)
ibd_genera=aggregateTaxa(ibd_taxa,ibd_lineages,taxon.level = "genus")
#> [1] "Number of higher-level taxa: 71"
#> [1] 71  7
groupBarplot(ibd_genera,groups=groups,randSampleNum=10)
#> [1] "Number of samples in group CD : 68"
#> [1] "Number of samples in group UC : 53"
#> [1] "Number of samples in group Control : 34"