plotTopicProportion: Plot the topic distribution in all specimens.

In PratheepaJ/diffTop: Differential topic analysis using latent Dirichlet allocation

Description

Plot the topic distribution in all specimens.

Usage

plotTopicProportion(
  ps,
  theta_aligned,
  K,
  col_names_theta_all = c("iteration", "Sample", "Topic", "topic.dis"),
  chain = 4,
  iterUse = 1000,
  SampleIDVarInphyloseq = "unique_names",
  design = ~pna
)

Arguments

ps	phyloseq object.
theta_aligned	List. returned object of thetaAligned().
K	integer. number of topics.
col_names_theta_all	Character vector. Column names for long formatted theta. An example is c("iteration", "Sample", "Topic", "topic.dis")
chain	integer. number of chains used in MCMC.
iterUse	integer. number of iterations used in each chain after subtracting warm-up samples.
SampleIDVarInphyloseq	Character. SampleID variable name in phyloseq object.
design	Factors of interests.

Value

A ggplot2 object. Histrogram of median of topic proportion in each sample.

PratheepaJ/diffTop documentation built on Dec. 18, 2021, 7:48 a.m.