Bubble heatmap of CAMERA-PR or ORA results from fuzzy c-means clustering

Generate a bubble heatmap from the results of nonparametric CAMERA-PR or ORA applied to the output of fuzzy c-means clustering.

Usage

plot_cluster_enrichment(
  x,
  set_ids = NULL,
  selected_tissues = c("adipose", "blood", "muscle"),
  selected_ome = c("transcript-rna-seq", "prot-pr", "prot-ph", "metab"),
  padj_cutoff = 0.05,
  n_top = 6L,
  column_title = NULL,
  filename
)

Arguments

x

a data.frame. Either FCM_CAMERA or FCM_ORA.

set_ids

character or NULL; one or more of x$set_id. The dataset x will be filtered to these sets. If NULL, the n_top most significant sets from each contrast will be selected.

selected_tissues

character; one or more tissues that will be used to create the heatmap. If multiple tissues are selected, only those terms tested in at least two tissues will be plotted.

selected_ome

character; the ome that will be used to create the heatmap.

padj_cutoff

numeric; cutoff in terms of p-value for an asterisk to be included

n_top

integer; if set_ids is NULL, the n_top most significant molecular signatures from each tissue and cluster will be selected.

column_title

character or NULL; title for the heatmap.

filename

character; path to a PDF file to save the heatmap.

Value

Nothing. The heatmap is saved to a PDF specified by filename.

Author

Tyler Sagendorf