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Plot UMAP Coordinates from a muscadet Object

Source: R/plots.R
plotUMAP.Rd

Visualize UMAP (Uniform Manifold Approximation and Projection) coordinates stored in a muscadet object. The function allows coloring by clusters and optionally adding cluster labels.

Usage

plotUMAP(
  x,
  partition = NULL,
  clusters = NULL,
  colors = NULL,
  title = "",
  lab.x = "UMAP 1",
  lab.y = "UMAP 2",
  add_clusters_labels = FALSE,
  point.size = 0.5,
  legend.point.size = 3,
  ...
)

Arguments

x

A muscadet object containing clustering data (using clusterMuscadet()).

partition

(Optional) Value specifying the clustering partition to plot (numeric or character). It should be either the resolution or the number of cluster (k) used for clustering depending on the clustering method (res_range or k_range with clusterMuscadet()). If both partition and clusters arguments are NULL (default), the assigned clusters for CNA calling (x@cnacalling$cluster) are used if available in x (see assignClusters()).

clusters

(Optional) A custom named vector of cluster assignments (integer named vector). Names must corresponds to cell names within the muscadet object x. If it contains less cells than the muscadet object x, the missing cells are filtered out and not displayed in the heatmap. If show_missing = FALSE only the provided cells with data in all omics will be displayed. If both partition and clusters arguments are NULL (default), the assigned clusters for CNA calling (x@cnacalling$cluster) are used if available in x (see assignClusters()).

colors

Vector of colors for the cluster annotation (character vector). If NULL (default), it uses predefined colors.

title

Character string for the title of the plot (character string). Default is an empty character string.

lab.x

Label for the x-axis (character string). Default is "UMAP 1".

lab.y

Label for the y-axis (character string). Default is "UMAP 2".

add_clusters_labels

Logical. If TRUE, adds the cluster names as text or boxed labels using add_labels(). Default is FALSE.

point.size

Numeric. Size of the points in the UMAP plot passed to ggplot2::geom_point(). Default is 0.5.

legend.point.size

Numeric. Size of the points in the legend of the UMAP plot. Default is 3.

...

Additional arguments passed to add_labels() providing an underlying geom for label names (geom_text(), geom_label(), geom_text_repel(), or geom_label_repel()).

Value

A ggplot object.

Examples

if (FALSE) { # \dontrun{
  p <- plotUMAP(muscadet_obj,
                partition = 0.6,
                title = "UMAP copy-number clusters")
  print(p)
} # }