Plot the topic distribution in all specimens.

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.