plot_wordcloud: Create wordcloud of terms associated with a miRNA name
In JulFriedrich/miRetrieve: miRNA Text Mining in Abstracts

Description Usage Arguments Details Value See Also

Create wordcloud of terms associated with a miRNA name.

plot_wordcloud(
  df,
  mir,
  min.freq = 1,
  max.terms = 20,
  tf.idf = FALSE,
  token = "words",
  ...,
  stopwords = stopwords_miretrieve,
  stopwords_ngram = TRUE,
  colours = "black",
  random.colour = TRUE,
  ordered.colour = FALSE,
  col.mir = miRNA,
  col.abstract = Abstract,
  col.pmid = PMID
)

`df`	Data frame containing miRNA names, abstracts, and PubMed-IDs.
`mir`	String. miRNA name of interest.
`min.freq`	Integer. Specifies least number of times a term must be associated with `mir` to be plotted.
`max.terms`	Integer. Maximum number of terms to plot.
`tf.idf`	Boolean. If `tf.idf = TRUE`, terms are weighed in a tf-idf fashion. miRNA names are considered as separate documents, and terms often associated with one miRNA, but not with other miRNAs get more weight. Cannot be used if `normalize = TRUE`. If `tf.idf = TRUE` and `normalize = TRUE`, `tf.idf = TRUE` is ignored.
`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.
`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'`.
`colours`	Vector of strings. Colours for wordcloud.
`random.colour`	Boolean. Taken from `wordcloud()` in the wordcloud package: "Choose colours randomly from `colours`. If false, the colour is chosen based on the frequency."
`ordered.colour`	Boolean. Taken from `wordcloud()` in the wordcloud package: "If true, then colours are assigned to words in order."
`col.mir`	Symbol. Column containing miRNA names.
`col.abstract`	Symbol. Column containing abstracts.
`col.pmid`	Symbol. Column containing PubMed-IDs.

Create wordcloud of terms associated with a miRNA name. miRNA names must be in a data frame df, while terms are taken from abstracts contained in df. Number of terms to plot is regulated by max.terms, while min.freq regulates the least number of times a term must be mentioned to be plotted. Terms can either be evaluated as their raw count, e.g. how often they are mentioned in conjunction with the miRNA of interest, or weighed in a tf-idf fashion. If tf.idf = TRUE, miRNA names are considered as separate documents, and terms often associated with one miRNA, but not with other miRNAs get more weight. plot_wordcloud() is based on the tools available in the wordcloud package.

Wordcloud of terms associated with a miRNA name.

plot_mir_terms(), wordcloud::wordcloud(), tidytext::unnest_tokens()

Other miR term functions: plot_mir_terms()

JulFriedrich/miRetrieve documentation built on Sept. 20, 2021, 11:37 p.m.