R: Compare terms uniquely associated with a miRNA name

compare_mir_terms_unique {miRetrieve}

R Documentation

Compare terms uniquely associated with a miRNA name

Description

Compare terms uniquely associated with a miRNA name over topics.

Usage

compare_mir_terms_unique(
  df,
  mir,
  top = 20,
  token = "words",
  ...,
  topic = NULL,
  stopwords = stopwords_miretrieve,
  stopwords_ngram = TRUE,
  normalize = TRUE,
  colour = "steelblue3",
  col.mir = miRNA,
  col.abstract = Abstract,
  col.topic = Topic,
  col.pmid = PMID,
  title = NULL
)

Arguments

`df`	Data frame containing miRNA names, abstracts, topics, and PubMed-IDs.
`mir`	String. miRNA name of interest.
`top`	Integer. Number of top terms to plot.
`token`	String. Specifies how abstracts shall be split up. Taken from `unnest_tokens()` in the tidytext package: "Unit for tokenizing, or a custom tokenizing function. Built-in options are "words" (default), "characters", "character_shingles", "ngrams", "skip_ngrams", "sentences", "lines", "paragraphs", "regex", (...), and "ptb" (Penn Treebank). If a function, should take a character vector and return a list of character vectors of the same length."
`...`	Additional arguments for tokenization, if necessary.
`topic`	Character vector. Optional. Specifies which topics to plot. If `topic = NULL`, all topics in `df` are plotted.
`stopwords`	Data frame containing stop words.
`stopwords_ngram`	Boolean. Specifies if stop words shall be removed from abstracts when using ngrams. Only applied when `token = 'ngrams'`.
`normalize`	Boolean. If `normalize = TRUE`, relative term frequency is plotted, denoting the relative number of papers with `mir` mentioning the term compared to all papers with `mir` mentioning the term. If `normalize = FALSE`, absolute term frequency is plotted, denoting the number of papers with `mir` the term is mentioned in.
`colour`	String. Colour of bar plot.
`col.mir`	Symbol. Column containing miRNAs.
`col.abstract`	Symbol. Column containing abstracts.
`col.topic`	Symbol. Column containing topics names.
`col.pmid`	Symbol. Column containing PubMed-IDs.
`title`	String. Plot title.

Details

Compare terms uniquely associated with a miRNA name over topics. miRNA names and topics must be in a data frame df, while terms are taken from abstracts contained in df. Number of top terms to choose is regulated by top. Terms are evaluated either as the number of times they are mentioned in all abstracts with the miRNA name of interest, or the number of times they are relatively mentioned compared to all abstracts with the miRNA name of interest. compare_mir_terms_unique() is based on the tools available in the tidytext package.

Value