correlate_factors_with_covariates: Plot correlation of factors with external covariates

In bioFAM/MOFA2: Multi-Omics Factor Analysis v2

Plot correlation of factors with external covariates

Description

Function to correlate factor values with external covariates.

Usage

correlate_factors_with_covariates(
  object,
  covariates,
  factors = "all",
  groups = "all",
  abs = FALSE,
  plot = c("log_pval", "r"),
  alpha = 0.05,
  return_data = FALSE,
  transpose = FALSE,
  ...
)

Arguments

object	a trained MOFA object.
covariates	data.frame:a data.frame where the samples are stored in the rows and the covariates are stored in the columns. Use row names for sample names and column names for covariate names. Columns values must be numeric. character vector:character vector with names of columns that are present in the sample metadata (samples_metadata(model)
factors	character vector with the factor name(s), or numeric vector with the index of the factor(s) to use. Default is 'all'.
groups	character vector with the groups names, or numeric vector with the indices of the groups of samples to use, or "all" to use samples from all groups.
abs	logical indicating whether to take the absolute value of the correlation coefficient (default is TRUE).
plot	character indicating whether to plot Pearson correlation coefficiens (plot="r") or log10 adjusted p-values (plot="log_pval").
alpha	p-value threshold
return_data	logical indicating whether to return the correlation results instead of plotting
transpose	logical indicating whether to transpose the plot
...	extra arguments passed to corrplot (if plot=="r") or pheatmap (if plot=="log_pval").

Value

A corrplot (if plot=="r") or pheatmap (if plot=="log_pval") or the underlying data.frame if return_data is TRUE

bioFAM/MOFA2 documentation built on June 12, 2024, 3:57 p.m.