Heatmap of module-clock effects

Rows are co-expression modules, columns are strata (or the comparison when there is no stratification), and each cell carries the effect with a star when the adjusted p-value clears sig_threshold. Modules live on different native scales, so the fill is the effect divided by a robust scale of its column while the printed number stays in the original units.

Usage

tage_module_heatmap(
  data,
  module_columns,
  group_column,
  reference_group,
  compare_groups = NULL,
  covariates = NULL,
  split_by = NULL,
  variance_strata = c("all_data", "subset"),
  standardize = TRUE,
  p_adjust = "BH",
  p_adjust_scope = "across_columns",
  sig_threshold = 0.05,
  module_set = NULL,
  module_functions = NULL,
  color_scale = c("robust", "absolute"),
  robust_pct = 95,
  limit = NULL,
  annotate = TRUE,
  digits = 2,
  title = "Module clocks",
  subtitle = NA,
  caption = NULL,
  base_size = 11,
  cell_height = 0.3,
  cell_width = 1.3,
  width = NULL,
  height = NULL,
  stats = NULL
)

Arguments

data

Data frame with one column per module clock.

module_columns

Module-clock columns.

group_column

Column holding the experimental groups.

reference_group

Reference level.

compare_groups

Levels compared against the reference; each becomes a facet. NULL uses every other level.

covariates, split_by, variance_strata, standardize, p_adjust, p_adjust_scope

Passed to tage_module_stats.

sig_threshold

Adjusted p-value below which a cell is starred.

module_set

Module set used for the row labels, one of "rodent", "multispecies" or "human"; see load_module_functions. Either this or module_functions is required: a module colour names a different module in each set.

module_functions

Named character vector, module column to function, used instead of the bundled annotation; character(0) labels the rows by module name only.

color_scale

"robust" divides each column by its robust_pct percentile of |effect| so differently scaled columns share one colour bar; "absolute" uses the raw effect.

robust_pct, limit

Percentile used by the robust scale, and the fill limit.

annotate

Whether to print the effect in each cell.

digits

Digits used for the printed effect.

title, subtitle, caption

Figure text.

base_size

Base font size.

cell_height, cell_width

Inches per module row and per column, used to size the canvas so that row labels stay legible as the module set grows.

width, height

Absolute figure size in inches, overriding cell_height and cell_width.

stats

Pre-computed tage_module_stats output.

Value

A ggplot object, with the statistics attached as the "tage_stats" attribute and the intended size as "tage_size"; see tage_save_plot.

Details

The statistics come from tage_module_stats.

See also

tage_module_stats, tage_clock_forest

Examples

if (FALSE) { # \dontrun{
tage_module_heatmap(results, module_columns = modules,
                    group_column = "Genotype", reference_group = "WT",
                    split_by = "Tissue")
} # }