`plotTopicProportion.Rd`

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 )

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. |

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