anno_word_cloud {simplifyEnrichment} | R Documentation

## Word cloud annotations

### Description

Word cloud annotations

### Usage

    anno_word_cloud(align_to, term, exclude_words = NULL, max_words = 10,
        word_cloud_grob_param = list(), fontsize_range = c(4, 16),
        bg_gp = gpar(fill = "#DDDDDD", col = "#AAAAAA"), side = c("right", "left"), ...)

### Arguments

`align_to` | How to align the annotations to the heatmap. Similar as in `anno_link`, the value of `align_to` can be a list of row indices or a categorical vector where each vector in the list corresponds to a word cloud. If it is a categorical vector, rows with the same level correspond to a same word cloud. If `align_to` is a categorical vector and `term` is a list, names of `term` should have overlap to the levels in `align_to`. When `align_to` is set as a categorical vector, normally the same value is set to `row_split` in the main heatmap so that each row slice can correspond to a word cloud.
`term` | The description text used for constructing the word clouds. The value should have the same format as `align_to`. If `align_to` is a list, `term` should also be a list. In this case, the length of vectors in `term` is not necessarily the same as in `align_to`. E.g. `length(term[[1]])` is not necessarily equal to `length(align_to[[1]]`. If `align_to` is a categorical vector, `term` should also be a character vector with the same length as `align_to`.
`exclude_words` | The words excluced for construcing word cloud.
`max_words` | Maximal number of words visualized in the word cloud.
`word_cloud_grob_param` | A list of graphics parameters passed to `word_cloud_grob`.
`fontsize_range` | The range of the font size. The value should be a numeric vector with length two. The minimal font size is mapped to word frequency value of 1 and the maximal font size is mapped to the maximal word frequency. The font size interlopation is linear.
`bg_gp` | Graphics parameters for controlling the background.
`side` | Side of the annotation relative to the heatmap.
`...` | Other parameters.

### Details

The word cloud annotation is constructed by `anno_link`.

If the annotation is failed to construct or no keyword is found, the function returns a `anno_empty` with 1px width.

### Examples

    gm = readRDS(system.file("extdata", "random_GO_BP_sim_mat.rds", package = "simplifyEnrichment"))
    go_id = rownames(gm)
    go_term = AnnotationDbi::select(GO.db::GO.db, keys = go_id, columns = "TERM")$TERM

    split = sample(letters[1:4], 100, replace = TRUE)
    align_to = split(1:100, split)
    term = lapply(letters[1:4], function(x) sample(go_term, sample(100:400, 1)))
    names(term) = letters[1:4]

    require(ComplexHeatmap)
    mat = matrix(rnorm(100*10), nrow = 100)
    Heatmap(mat, cluster_rows = FALSE, row_split = split,
    	right_annotation = rowAnnotation(foo = anno_word_cloud(align_to, term)))

[Package simplifyEnrichment version 1.2.0 Index]