add_cluster_annotation: add_cluster_annotation

In jrboyd/seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

add_cluster_annotation

Description

adds rectangle boxes proportional to cluster sizes of heatmap with optional labels.

Usage

add_cluster_annotation(
  cluster_ids,
  p = NULL,
  xleft = 0,
  xright = 1,
  rect_colors = c("black", "gray"),
  text_colors = rev(rect_colors),
  show_labels = TRUE,
  label_angle = 0,
  row_ = "id",
  cluster_ = "cluster_id"
)

Arguments

cluster_ids	Vector of cluster ids for each item in heatmap. Should be sorted by plot order for heatmap.
p	Optionally an existing ggplot to add annotation to.
xleft	left side of cluster annotation rectangles. Default is 0.
xright	right side of cluster annotation rectangles. Default is 1.
rect_colors	colors of rectangle fill, repeat to match number of clusters. Default is c("black", "gray").
text_colors	colors of text, repeat to match number of clusters. Default is reverse of rect_colors.
show_labels	logical, shoud rectangles be labelled with cluster identity. Default is TRUE.
label_angle	angle to add clusters labels at. Default is 0, which is horizontal.
row_	variable name mapped to row, likely id or gene name for ngs data. Default is "id" and works with ssvFetch* outputs.
cluster_	variable name to use for cluster info. Default is "cluster_id".

Value

A ggplot with cluster annotations added.

Examples

data(CTCF_in_10a_profiles_dt)
#simplest uses
add_cluster_annotation(factor(c(rep("A", 3), "B")))
p = ggplot() + coord_cartesian(xlim = c(0,10))
add_cluster_annotation(factor(c(rep("A", 3), "B")), p)

#intended use with ssvSignalHeatmap
clust_dt = ssvSignalClustering(CTCF_in_10a_profiles_dt, nclust = 3)
assign_dt = unique(clust_dt[, .(id, cluster_id)])[order(id)]
p_heat = ssvSignalHeatmap(clust_dt, show_cluster_bars = FALSE)
add_cluster_annotation(assign_dt$cluster_id, p_heat,
  xleft = -500, xright = -360, rect_colors = rainbow(3), text_colors = "gray")

#when colors are named, the names are used rather that just the order
rect_colors = safeBrew(assign_dt$cluster_id)
text_colors = safeBrew(assign_dt$cluster_id, "greys")
p_clusters = add_cluster_annotation(assign_dt$cluster_id,
  rect_colors = rect_colors, text_colors = text_colors)
#specialized use as plot outside of heatmap
p1 = assemble_heatmap_cluster_bars(plots = list(p_clusters, p_heat), rel_widths = c(1, 3))

#when colors are named, the names are used rather that just the order
#these plots will be identical even though order of colors changes.
rect_colors = rect_colors[c(2, 3, 1)]
text_colors = text_colors[c(3, 1, 2)]
p_clusters = add_cluster_annotation(assign_dt$cluster_id,
  rect_colors = rect_colors, text_colors = text_colors)
#specialized use as plot outside of heatmap
p2 = assemble_heatmap_cluster_bars(plots = list(p_clusters, p_heat), rel_widths = c(1, 3))

cowplot::plot_grid(p1, p2, ncol = 1)

jrboyd/seqsetvis documentation built on Oct. 15, 2024, 11:28 p.m.