ht_clusters: Visualize the similarity matrix and the clustering

In jokergoo/simplifyEnrichment: Simplify Functional Enrichment Results

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 = TRUE,
    min_term = round(nrow(mat)*0.01),
    order_by_size = FALSE,
    stat = "pvalue",
    min_stat = ifelse(stat == "count", 5, 0.05),
    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 97.5^th percentile of the similarity values. The value can also be a color mapping function generated by colorRamp2.
draw_word_cloud	Whether to draw the word clouds.
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.
stat	Type of value for mapping to the font size of keywords in the word clouds. There are two options: "count": simply number of keywords; "pvalue": enrichment on keywords is performed (by fisher's exact test) and -log10(pvalue) is used to map to font sizes.
min_stat	Minimal value for stat for selecting keywords.
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 font size interpolation 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

## Not run: 
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)

## End(Not run)

jokergoo/simplifyEnrichment documentation built on Nov. 3, 2023, 2:57 p.m.