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# plot box plots of marker median or mean

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

`plot_marker_boxplot()` generates faceted box plots of aggregated expression per sample grouped by a grouping of interest for each marker-cluster combination.

## Usage

    plot_marker_boxplot(
      fcd,
      marker = NULL,
      expr_slot = "orig",
      cluster_slot = "Phenograph_pca_orig_k_60",
      cluster_var = "metaclusters",
      cluster_to_show = NULL,
      group_var,
      sample_var,
      fun = "median",
      facet_by_clustering = F,
      facet_ncol = 5,
      color_palette = cluster_palette,
      dot_size = 2
    )

## Arguments

fcd

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

marker

  marker in provided expr_slot that should be included in plotting. By default all features are plotted.

expr_slot

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

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

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

group_var

  string indicating variable name in cell_anno that should be used to group samples in sample_var

sample_var

  string indicating variable name in cell_anno that defines sample IDs to be used.

fun

  string indicating which aggregation of expression should be performed for each sample. Needs to be one out of "median" (default) or "mean".

facet_by_clustering

  logical indicating how to structure faceting of the plot. If set to FALSE (default) plot will be faceted by markers and clusters (or cell populations) are shown on x-axis. If set to TRUE, it is the other way around.

facet_ncol

  Number of columns to be used for faceting.

color_palette

  vector of colors that should be used to fill box plots.

dot_size

  numeric indicating the size of the dots.

## Value

A faceted ggplot showing box plots of aggregated expression per sample grouped by group_var.

## Details

plot_marker_boxplot