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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