R: Compare count of terms associated with a miRNA name over...

compare_mir_terms {miRetrieve}

R Documentation

Compare count of terms associated with a miRNA name over various topics

Description

Compare count of top terms associated with a miRNA name over various topics.

Usage

compare_mir_terms(
  df,
  mir,
  top = 20,
  token = "words",
  ...,
  topic = NULL,
  shared = TRUE,
  normalize = TRUE,
  stopwords = stopwords_miretrieve,
  stopwords_ngram = TRUE,
  position = "dodge",
  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 topics to plot. If `topic = NULL`, all topics in `df` are plotted.
`shared`	Boolean. If `shared = TRUE`, only terms that are shared between all topics are plotted.
`normalize`	Boolean. If `normalize = TRUE`, normalizes the number of abstracts to the total number of abstracts with a miRNA name in a topic.
`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'`.
`position`	Character vector. Vector containing either "dodge" or "facet". Determines if bar plots are on top of or next to each other.
`col.mir`	Symbol. Column containing miRNA names.
`col.abstract`	Symbol. Column containing abstracts.
`col.topic`	Symbol. Column containing topic names.
`col.pmid`	Symbol. Column containing PubMed-IDs.
`title`	String. Plot title.

Details

Compare count of top terms associated with a miRNA name over various 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 plot is regulated by top. Terms can either be evaluated as their raw count, e.g. in how many abstracts they are mentioned in conjunction with the miRNA name, or as their relative count, e.g. in how many abstracts containing the miRNA they are mentioned compared to all abstracts containing the miRNA. compare_mir_terms() is based on the tools available in the tidytext package.

Value