ht_clusters {simplifyEnrichment}R Documentation

Visualize the similarity matrix and the clustering

Description

Visualize the similarity matrix and the clustering

Usage

ht_clusters(
    mat,
    cl,
    dend = NULL,
    col = c("white", "red"),
    
    # arguments that control the word cloud annotation
    draw_word_cloud = is_GO_id(rownames(mat)[1]) || !is.null(term),
    term = NULL,
    min_term = round(nrow(mat)*0.01),
    order_by_size = FALSE,
    exclude_words = character(0),
    max_words = 10,
    word_cloud_grob_param = list(),
    fontsize_range = c(4, 16),
    bg_gp = gpar(fill = "#DDDDDD", col = "#AAAAAA"),
    
    # arguments that control the heatmaps
    column_title = NULL,
    ht_list = NULL,
    use_raster = TRUE,
    run_draw = TRUE,
    ...)

Arguments

mat

A similarity matrix.

cl

Cluster labels inferred from the similarity matrix, e.g. from cluster_terms or binary_cut.

dend

Used internally.

col

A vector of colors that map from 0 to the 95^th percentile of the similarity values.

draw_word_cloud

Whether to draw the word clouds.

term

The full name or the description of the corresponding GO IDs.

min_term

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

order_by_size

Whether to reorder 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

Graphics parameters for controlling word cloud annotation background.

column_title

Column title for the heatmap.

ht_list

A list of additional heatmaps added to the left of the similarity heatmap.

use_raster

Whether to write the heatmap as a raster image.

run_draw

Internally used.

...

Other arguments passed to draw,HeatmapList-method.

Value

A HeatmapList-class object.

Examples

mat = readRDS(system.file("extdata", "random_GO_BP_sim_mat.rds",
    package = "simplifyEnrichment"))
cl = binary_cut(mat)
ht_clusters(mat, cl, word_cloud_grob_param = list(max_width = 80))
ht_clusters(mat, cl, word_cloud_grob_param = list(max_width = 80),
    order_by_size = TRUE)

[Package simplifyEnrichment version 1.3.0 Index]