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

plot_heatmap.Rd

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