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Plot UMAP with Discrete or Continuous Coloring

Source: R/plots.R
plot_umap.Rd

This function plots a UMAP embedding with points colored by either discrete or continuous cell information. The function provides options for sorting the cells based on the coloring variable, adjusting point size and alpha, and customizing the color scheme for both discrete and continuous coloring.

Usage

plot_umap(
  umap_embedding,
  cell_info,
  mtd_name,
  cell_sort_order = c("lowest", "highest", "default"),
  scale_values = FALSE,
  cell_size = 0.3,
  cell_alpha = 0.8,
  legend_text_size = 10,
  legend_key_size = 0.5,
  axis_text_size = 10,
  show_labels = TRUE,
  label_size = 10,
  colourbar_width = 50,
  discrete_colors = NULL,
  continuous_colors = NULL
)

Arguments

umap_embedding

A matrix or data frame containing the UMAP coordinates of the cells. It should have two columns corresponding to UMAP1 and UMAP2.

cell_info

A vector containing the information to color the cells by. It can be either a factor/character vector for discrete coloring or a numeric vector for continuous coloring. The length of this vector should match the number of rows in umap_embedding.

mtd_name

A string specifying the name of the metadata variable to be used in the legend.

cell_sort_order

A character vector specifying the order of cells based on the cell_info variable. For discrete coloring, it should contain the unique values of cell_info in the desired order. For continuous coloring, it can be either "lowest", "highest" or "default" to sort cells by the cell_info values in ascending, descending or no particular order, respectively.

scale_values

A logical indicating whether to scale the cell_info values between 0 and 1 for continuous coloring. Defaults to FALSE.

cell_size

A numeric value specifying the size of the points in the plot. Defaults to 0.3.

cell_alpha

A numeric value between 0 and 1 specifying the transparency of the points in the plot. Defaults to 0.8.

legend_text_size

A numeric value specifying the size of the text in the legend. Defaults to 10.

legend_key_size

A numeric value specifying the size of the legend keys for discrete coloring. Defaults to 0.5.

axis_text_size

A numeric value specifying the size of the axis text in the plot. Defaults to 10.

show_labels

A logical indicating whether to show labels for discrete groups. Defaults to TRUE.

label_size

A numeric value specifying the size of the labels for discrete groups. Defaults to 10.

colourbar_width

A numeric value specifying the width of the colorbar for continuous coloring. Defaults to 50 points. If set to 0, the colorbar will be hidden.

discrete_colors

A list of color vectors for discrete coloring, where the names of the list correspond to the number of unique values in cell_info. If NULL, the default ggplot2 colors will be used.

continuous_colors

A vector of colors for continuous coloring. If NULL, the default ggplot2 colors will be used.

Value

A ggplot object representing the UMAP plot with the specified coloring and customization options.