Compute associations between TF module scores and clinical metadata

This function tests for associations between transcription factor (TF) module scores and available clinical traits. Numeric traits are correlated with each module (Pearson or Spearman) and shown as a labeled heatmap. If plot_grid = TRUE, categorical traits are additionally tested with one-way ANOVA (Tukey HSD post-hoc) and shown as boxplot grids. All plots are saved in the Results/ directory.

Usage

compute.metadata.association(
  tfs.modules,
  coldata,
  pval = 0.05,
  corr_method = "p",
  file.name,
  width = 20,
  height = 8,
  ncol = 5,
  y_min = 0,
  y_max = 0.5,
  plot_grid = F,
  width_grid = 18,
  height_grid = 10
)

Arguments

tfs.modules

A numeric matrix or data frame of TF module scores across samples. Typically the output from compute.WTCNA(). Rows represent samples, columns represent TF modules.

coldata

A data frame containing clinical traits (both categorical and numerical) for the same samples. Row names should match those of tfs.modules.

pval

A numeric threshold (default = 0.05) to determine statistical significance. Only associations with p-values below this threshold are considered significant in the heatmap.

corr_method

Character string specifying the correlation method to use for continuous variables. Options are "p" for pearson and "s" for spearman. Default is "p".

file.name

Character. Base file name for saving plots of results.

width

A numeric value indicating the width (in inches) of the output heatmap plot (default = 20).

height

A numeric value indicating the height (in inches) of the output heatmap plot (default = 8).

ncol

Integer. Number of columns in the grid of association boxplots.

y_min

Numeric. Lower y-axis limit for grid boxplots.

y_max

Numeric. Upper y-axis limit for grid boxplots.

plot_grid

Logical; if TRUE, tests categorical traits with ANOVA and saves boxplot grids.

width_grid

Numeric width of the grid plot output.

height_grid

Numeric height of the grid plot output.

Value

Called for its side effects. Saves to the Results/ directory:

• TF.modules_metadata_<file.name>.pdf: a labeled heatmap of module-trait correlations for numeric traits (only associations with p-value < pval are annotated).

• ANOVA_boxplot_summary_<file.name>_<trait>.svg (if plot_grid = TRUE): one boxplot grid per categorical trait with the significant modules.

Examples

data("network.tuto")
data("traitdata.tuto")

compute.metadata.association(
  tfs.modules = network.tuto[[1]],
  coldata = traitdata.tuto,
  pval = 0.05,
  file.name = 'Tutorial',
  width = 15,
  height = 10
)