groupBarplot | R Documentation |
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, ... )
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() |
Note that taxa are always summed across all samples, also in the presence of a group membership vector, unless sumGroupwise is true.
if extendTaxonColorMap is true, the taxon color map is returned
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) # sum taxa group-wise for sorting instead across all samples groupBarplot(ibd_taxa,groups=groups,sumGroupwise=TRUE, legend.hidegroups=TRUE) data(ibd_lineages) ibd_genera=aggregateTaxa(ibd_taxa,ibd_lineages,taxon.level = "genus") groupBarplot(ibd_genera,groups=groups,randSampleNum=10)
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