plotStackedBars: Plot stacked abundace barplots

In microresearcher/MicroVis: Microbiome Analysis and Visualization

Plot stacked abundace barplots

Description

Plot stacked abundace barplots

Usage

plotStackedBars(
  dataset = NULL,
  relative = T,
  factor = NULL,
  stratify = F,
  bySample = F,
  allSamples = F,
  paired_ids = c(),
  unfiltered = T,
  label_unknown = T,
  rank = NA,
  top = 15,
  top_by = "mean",
  ftlist = c(),
  plotSigs = F,
  alpha = 0.05,
  separateLegend = F
)

Arguments

dataset	MicroVis dataset. Defaults to the active dataset
relative	Whether to plot relative abundance. Defaults to TRUE
factor	Factor to group samples by
stratify	Whether to stratify the groups. Defaults to FALSE
bySample	Whether to show a bar for each sample instead of aggregating samples by groups. Defaults to FALSE
allSamples	Whether to plot a single graph for all the samples in the dataset. Defaults to FALSE
paired_ids	Plot samples paired by "factor", with each pair having a unique combination of IDs determined by this variable (as a vector)
unfiltered	Whether to use data before or after filtering out features. Defaults to TRUE (uses data before filtering)
label_unknown	Whether to group unknown taxa separate. Defaults to TRUE
rank	Rank at which to use features
top	Number of features to show based on greatest relative abundance. Defaults to top 15 features by relative abundance
top_by	Select the top features either by the max, min, or mean relative abundance in the groups, or the summed relative abundance across all groups. Defaults to mean (in other words, for each feature its mean relative abundance values across the samples will be used to determine whether it is a top feature).
ftlist	(Optional) List of features to consider. Defaults to all features at the rank
plotSigs	Plot only the significant features? Defaults to FALSE
alpha	Significance threshold for selecting significant features. Defaults to 0.05
separateLegend	Whether to separate the legend from the plot. Defaults to FALSE

Value

Stacked bar plot of feature abundances of selected features with the other features lumped into an "Other" category

microresearcher/MicroVis documentation built on Feb. 8, 2024, 10:59 a.m.