Visualize Dimensionality Reduction Results — sig_visualise

This function creates a scatter plot of the results from a dimensionality reduction technique (e.g., UMAP or PCA). The plot can include optional metadata features such as color, fill, and shape for further distinction of sample groups.

Usage

sig_visualise_dimred(
  dimred,
  col_sample = "sample",
  col_dim1 = "dim1",
  col_dim2 = "dim2",
  metadata = NULL,
  col_fill = NULL,
  col_colour = NULL,
  col_shape = NULL,
  title = "Dimensionality Reduction",
  xlab = col_dim1,
  ylab = col_dim2
)

Arguments

dimred: A data frame containing the dimensionality reduction results with at least columns for the two dimensions (col_dim1, col_dim2) and a sample identifier (col_sample).
col_sample: A string specifying the column name in dimred that identifies the samples. Default is "sample".
col_dim1: A string specifying the column name in dimred for the first dimension. Default is "dim1".
col_dim2: A string specifying the column name in dimred for the second dimension. Default is "dim2".
metadata: Optional. A data frame with metadata corresponding to the samples, with columns for the sample identifiers (col_sample) and other optional aesthetic mappings (col_fill, col_colour, col_shape).
col_fill: Optional. A string specifying the column name in metadata for the fill aesthetic. Default is NULL.
col_colour: Optional. A string specifying the column name in metadata for the color aesthetic. Default is NULL.
col_shape: Optional. A string specifying the column name in metadata for the shape aesthetic. Default is NULL.
title: A string specifying the title of the plot. Default is "Dimensionality Reduction".
xlab: A string specifying the label for the x-axis. Default is the value of col_dim1.
ylab: A string specifying the label for the y-axis. Default is the value of col_dim2.

Value

A ggplot object representing the dimensionality reduction plot.

Examples

# Example UMAP data
dimred <- example_umap()
metadata <- example_umap_metadata()
sig_visualise_dimred(dimred, metadata = metadata, col_colour = "dataset")