Draw wordcloud using the collection of RAVs' MeSH terms — drawWordcloud • GenomicSuperignature

Plot a word cloud using the remaining MeSH terms in the selected RAV after user-defined filtering.

drawWordcloud(
  RAVmodel,
  ind,
  rm.noise = NULL,
  scale = c(3, 0.5),
  weighted = TRUE,
  drop = NULL,
  filterMessage = TRUE
)

Arguments

RAVmodel: PCAGenomicSignatures object
ind: An index of the RAV you want to draw wordcloud.
rm.noise: An integer. Under the default (rm.noise=NULL), if cluster size (= s) is smaller than 8, rm.noise = floor(s*0.5). For clusters with >= 8 PCs, rm.noise = 4. If rm.noise = 0, all the MeSH terms in RAV will be used to draw wordcloud.
scale: A scale argument for wordcloud function
weighted: A logical. If TRUE (default), MeSH terms from each study are weighted based on the variance explained by the principle component of the study contributing to a given RAV.
drop: A character vector containing MeSH terms to be excluded from word cloud. Under the default (NULL), manually selected non-informative MeSH terms are excluded, which can be viewed through data(droplist).
filterMessage: A logical. Under the default TRUE, any output RAV belong to the filtering list will give a message. Silence this message with filterMessage=FALSE. You can check the filter list using data("filterList").

Value

A word cloud with the MeSH terms associated with the given cluster.

Examples

data(miniRAVmodel)
drawWordcloud(miniRAVmodel, 1139)
#> RAV1139 can be filtered based on GSEA_PLIERpriors
#> Warning: Leukemia, Lymphocytic, Chronic, B-Cell could not be fit on page. It will not be plotted.