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# plot_marker_dotplot

Source: `R/data_visualization.R`
`plot_marker_dotplot.Rd`

`plot_marker_dotplot()` generates a classical scatter plot of two markers

## Usage

    plot_marker_dotplot(
      fcd,
      expr_slot = "orig",
      marker_x,
      marker_y,
      cluster_slot,
      cluster_var,
      cluster_to_show = NULL,
      group_var = NULL,
      order = F,
      seed = 91,
      color_palette = cluster_palette,
      dot_size = 2,
      alpha = 1,
      title = ""
    )

## Arguments

fcd

  flow cytometry data set, that has been subjected to clustering or cell type label prediction with cyCONDOR

expr_slot

  expr_slot from which to take marker expression values, default is "orig". Corrected input data should be handled cautiously.

marker_x

  marker name in expr slot of which transformed expression is shown on x-axis.

marker_y

  marker name in expr slot of which transformed expression is shown on y-axis.

cluster_slot

  string specifying which clustering slot to use to find variable specified in cluster_var.

cluster_var

  string specifying variable name in cluster_slot that identifies cell population labels to be used (e.g. clusters, metaclusters or predicted labels).

cluster_to_show

  (optional) vector of characters indicating levels in cluster_var that should be included for plotting. By default all groups are plotted.

group_var

  (optional) string indicating variable name in cell_anno that should be used to color dots in plot. If not used, dots are clustered by cluster_var.

order

  logical if you want to order the dots in the plot by the variable used for coloring (TRUE). If set to FALSE (default), order of the cells is randomized.

seed

  a seed is set for reproducibility of the plotting result.

color_palette

  vector of colors that should be used to color dots.

dot_size

  numeric indicating the size of the dots.

alpha

  transparency of the dots.

title

  Title of the plot.

## Value

The function returns a scatter plot of two features available in the expression matrix. By default, dots are colored by cell population label provided in cluster_var. If coloring by a metadata is wanted instead, a group_var can be defined. Further, if only a selection of levels available in cluster_var should be included in plotting, a vector of labels of interest can be provided to cluster_to_show argument.

## Details

plot_marker_dotplot