plot_heatmap: makes heatmap from all experiments, filter on a single metric...
In TeamMacLean/pepdiff: Analysing TSL PRM Peptide Data

plot_heatmap

R Documentation

makes heatmap from all experiments, filter on a single metric and sig value

Description

reduces dataframes and makes long list, makes a basic heatmap. Use 'fold_change_matrix()' to extract data in a heatmappable format

Usage

plot_heatmap(
  l,
  sig_level = 0.05,
  metric = "bootstrap_t_fdr",
  log = TRUE,
  base = 2,
  col_order = NULL,
  sig_only = TRUE,
  pal = "RdBu",
  lgd_x = 1.7,
  lgd_y = 1,
  padding = c(0, 0, 0, 3)
)

Arguments

`l`	list of results, usually from 'compare_many()'
`sig_level`	significance level cutoff
`metric`	the test metric used to determine significance one of: 'bootstrap_t_p_val', 'bootstrap_t_fdr' 'wilcoxon_p_val', 'wilcoxon_fdr' 'kruskal_p_val', 'kruskal_fdr' 'rank_prod_p1_p_val', 'rank_prod_p2_p_val', 'rank_prod_p1_fdr', 'rank_prod_p2_fdr'.
`log`	whether to log the data
`base`	base used in logging (default = 2)
`col_order`	specify a column order for the plot, default is names(l)
`sig_only`	return only rows with 1 or more values significant at 'sig_level' of 'metric'
`pal`	cbrewer palette to use "RdBu", needs minimum 11 colours
`lgd_x`	x offset of legend placement in 'in' units
`lgd_y`	y offset of legend placement in 'in' units
`padding`	vector of padding values to pass to ComplexHeatmap::draw for padding of heatmap sections