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dimensionality reduction plot with density distribution

Source: R/data_visualization.R
plot_dim_density.Rd

plot_dim_density() plots the density distribution of each level of a grouping variable on top of dimensionality reduction plot. At the moment, only UMAP visualization is supported

Usage

plot_dim_density(
  fcd,
  reduction_method = "umap",
  reduction_slot,
  group_var,
  title = "",
  dot_size = 0.1,
  alpha = 0.2,
  color_density = c("Blues", "Oranges", "Reds")
)

Arguments

fcd

flow cytometry data set comprising dimensionality reduction calculated with cyCONDOR.

reduction_method

string specifying which dimensionality reduction method to use. At the moment, only "umap" is supported.

reduction_slot

string specifying reduction name in reduction_method to use for visualization, e.g. "pca_orig".

group_var

string indicating variable name in cell_anno for which density distribution will be plotted for each level in group_var.

title

character string, title of the plot

dot_size

size of the background dots.

alpha

transparency of the background dots.

color_density

vector of strings indicating the color palette from RColorBrewer to be used for the density gradient. A names vector using levels in group_var allows the assignment of a specific color to a group level. If vector is not names, entries will be assigned to groups in alphabetic order and color palettes will be reused if vector has less colors than levels in group_var

Value

Density Plot

Details

plot_dim_density