ssvHeatmap2: seqsetvis improved Heatmap

In jrboyd/ssvRecipes: Recipes using seqsetvis

seqsetvis improved Heatmap

Description

An upgrade to setsetvis' ssvSignalHeatmap() function accepts a standard wide matrix with some colname an rowname assumptions.

Usage

ssvHeatmap2(
  mat,
  treatment_ordering = NULL,
  replicate_ordering = NULL,
  treatment_space_size = 0.1,
  treatment_label_size = 8,
  main_heights = c(8, 1, 2, 2),
  main_widths = c(2, 0.1, 0.2, 0.2, 1.8),
  cluster_ = "cluster_id",
  treatment_ = "sample",
  replicate_ = "x",
  column_ = "column",
  row_ = "id",
  fill_ = "y",
  fill_label = fill_,
  fill_limits = NULL,
  nclust = 5,
  main_title = "Heatmap",
  main_title.x = 0.02,
  main_title.y = 0.98,
  main_title.hjust = 0,
  main_title.vjust = 1,
  side_plot_type = c("lines1", "lines2", "bars1", "bars2")[1],
  side_plot_FUN = NULL,
  side_plot_ylab = "",
  side_plot_ylab_width = 0.1,
  heatmap_colors = rev(seqsetvis::safeBrew(5, pal = "spectral")),
  symm_colors = TRUE,
  side_plot_colors = NULL
)

Arguments

mat	numeric matrix with row and column names set. see details.
treatment_ordering	order used for columns and side plots. default NULL causes order of supplied data to be used.
replicate_ordering	order used for sub columns and side plots ticks. default NULL causes order of supplied data to be used.
treatment_space_size	numeric >=0. size of white space separating heatmap groups. Default is 0.1
treatment_label_size	numeric > 0. size of text to label groups with, default is 8.
main_heights	numeric of length 4. controls size of heatmap body, axis ticks, group labels, and scale portion.
main_widths	numeric of length 5. controls size of heatmap body, spacer, cluster bars, cluster connector, and aggregate plots
cluster_	variable for cluster assignment
treatment_	name of conditions/treatment groups. appears in plots.
replicate_	name of replicate identifier. appears in plots.
column_	name of heatmap column variable - no effect if supplying mat as matrix.
row_	name of heatmap row variable - no effect if supplying mat as matrix.
fill_	name of heatmap fill variable - no effect if supplying mat as matrix.
fill_label	labl for fill legend
fill_limits	If not NULL, imposes limits on data.
nclust	numeric number of clusters
main_title	title appearing above assembled figure.
main_title.x	main title x position
main_title.y	main title y position
main_title.hjust	main title hjust
main_title.vjust	main title vjust
side_plot_type	plotting method for aggregate side plots. one of c("lines1", "lines2", "bars1", "bars2").
side_plot_FUN	overrides sideplot type. supplied function is executed once per cluster and must return a ggplot. call is: side_plot_FUN(clust, i, fill_, replicate_, treatment_, cluster_, side_plot_colors) Where clust is a tidy data.table containing 4 variables_, i is cluster id.
side_plot_ylab	label for y-axis of side plot
side_plot_ylab_width	relative wide of y-lab as a fraction of 1, Default is .1
heatmap_colors	colors for heatmap, default uses spectral palette from color brewer.
symm_colors	If TRUE, limits will be symmetrical.
side_plot_colors	colors for side_plot. must be same length as number of treatment groups. default uses dark2 palette from color brewer.

Details

colnames must contain a single "_".

Condition or treatment groups should precede the "_".

A unique replicate identifier should follow the "_". Replicate identifiers should be unique within each treatment group.

valid colnames:

A_1, A_2, B_1, B_2

A_1, A_2, A_3

A_1, B_1, C_1, C_2

rownames must be set and be unique.

Value

a ssvH2 object. print() this object for help.

Examples

res = ssvHeatmap2(heatmap_demo_matrix)
print(res)
plot(res)

res.lim = ssvHeatmap2(heatmap_demo_matrix, fill_limits = c(-20, 20))
plot(res.lim)

res2 = ssvHeatmap2(heatmap_demo_matrix, side_plot_ylab = 'y-value')
plot(res2)

jrboyd/ssvRecipes documentation built on May 22, 2022, 7:07 a.m.