simplifyGO {simplifyEnrichment} | R Documentation

## Simplify Gene Ontology (GO) enrichment results

### Description

Simplify Gene Ontology (GO) enrichment results

### Usage

    simplifyGO(mat, method = "binary_cut", control = list(),
        plot = TRUE, term = NULL, verbose = TRUE,
        column_title = qq("@{nrow(mat)} GO terms clustered by '@{method}'"),
        ht_list = NULL, ...)

### Arguments

`mat` | A GO similarity matrix.
`method` | Method for clustering the matrix. See `cluster_terms`.
`control` | A list of parameters for controlling the clustering method, passed to `cluster_terms`.
`plot` | Whether to make the heatmap.
`term` | The full name or the description of the corresponding GO IDs. The values are automatically extracted if it is not provided.
`column_title` | Column title for the heatmap.
`verbose` | Whether to print messages.
`ht_list` | A list of additional heatmaps added to the left of the similarity heatmap.
`...` | Arguments passed to `ht_clusters`.

### Details

This is basically a wrapper function that it first runs `cluster_terms` to cluster GO terms and then runs `ht_clusters` to visualize the clustering.

The arguments in `simplifyGO` passed to `ht_clusters` are:

`draw_word_cloud`

  Whether to draw the word clouds.

`min_term`

  Minimal number of GO terms in a cluster. All the clusters with size less than `min_term` are all merged into one single cluster in the heatmap.

`order_by_size`

  Whether to reorder GO clusters by their sizes. The cluster that is merged from small clusters (size < `min_term`) is always put to the bottom of the heatmap.

`exclude_words`

  Words that are excluded in the word cloud.

`max_words`

  Maximal number of words visualized in the word cloud.

`word_cloud_grob_param`

  A list of graphic 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`

  Graphic parameters for controlling the background of word cloud annotations.

### Value

A data frame with three columns: GO IDs, GO term names and cluster labels.

### See Also

`simplifyGOFromMultipleLists` which performs simplifyGO analysis with multiple lists of GO IDs.

### Examples

    set.seed(123)
    go_id = random_GO(500)
    mat = GO_similarity(go_id)
    df = simplifyGO(mat, word_cloud_grob_param = list(max_width = 80))
    head(df)

[Package simplifyEnrichment version 1.4.0 Index]