plot_dimred: Plot dimensionality reduction based on MOFA factors

In bioFAM/MOFA2: Multi-Omics Factor Analysis v2

Plot dimensionality reduction based on MOFA factors

Description

Plot dimensionality reduction based on MOFA factors

Usage

plot_dimred(
  object,
  method = c("UMAP", "TSNE"),
  groups = "all",
  show_missing = TRUE,
  color_by = NULL,
  shape_by = NULL,
  color_name = NULL,
  shape_name = NULL,
  label = FALSE,
  dot_size = 1.5,
  stroke = NULL,
  alpha_missing = 1,
  legend = TRUE,
  rasterize = FALSE,
  return_data = FALSE,
  ...
)

Arguments

object	a trained MOFA object.
method	string indicating which method has been used for non-linear dimensionality reduction (either 'umap' or 'tsne')
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.
show_missing	logical indicating whether to include samples for which shape_by or color_by is missing
color_by	specifies groups or values used to color the samples. This can be either: (1) a character giving the name of a feature present in the training data. (2) a character giving the same of a column present in the sample metadata. (3) a vector of the same length as the number of samples specifying discrete groups or continuous numeric values.
shape_by	specifies groups or values used to shape the samples. This can be either: (1) a character giving the name of a feature present in the training data, (2) a character giving the same of a column present in the sample metadata. (3) a vector of the same length as the number of samples specifying discrete groups.
color_name	name for color legend.
shape_name	name for shape legend.
label	logical indicating whether to label the medians of the clusters. Only if color_by is specified
dot_size	numeric indicating dot size.
stroke	numeric indicating the stroke size (the black border around the dots, default is NULL, infered automatically).
alpha_missing	numeric indicating dot transparency of missing data.
legend	logical indicating whether to add legend.
rasterize	logical indicating whether to rasterize plot using geom_point_rast
return_data	logical indicating whether to return the long data frame to plot instead of plotting
...	extra arguments passed to run_umap or run_tsne.

Details

This function plots dimensionality reduction projections that are stored in the dim_red slot. Typically this contains UMAP or t-SNE projections computed using run_tsne or run_umap, respectively.

Value

Returns a ggplot2 object or a long data.frame (if return_data is TRUE)

Examples

# Using an existing trained model on simulated data
file <- system.file("extdata", "model.hdf5", package = "MOFA2")
model <- load_model(file)

# Run UMAP
model <- run_umap(model)

# Plot UMAP
plot_dimred(model, method = "UMAP")

# Plot UMAP, colour by Factor 1 values
plot_dimred(model, method = "UMAP", color_by = "Factor1")

# Plot UMAP, colour by the values of a specific feature
plot_dimred(model, method = "UMAP", color_by = "feature_0_view_0")

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