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# Heatmap of scaled expression by cell population

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

`plot_marker_HM()` generates a heatmap of scaled mean marker expression for each cell population.

## Usage

    plot_marker_HM(
      fcd,
      expr_slot = "orig",
      marker_to_exclude = NULL,
      cluster_slot,
      cluster_var,
      cluster_rows = FALSE,
      cluster_cols = FALSE,
      maxvalue = NULL,
      size = 10,
      title = "Heatmap of scaled expression"
    )

## 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_to_exclude

  (optional) vector of characters indicating which features in expression matrix should not be included in the heatmap.

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_rows

  logical indicating if heatmap rows should be clustered (default: FALSE).

cluster_cols

  logical indicating if heatmap columns should be clustered (default: FALSE).

maxvalue

  max value for the coloring (default: NULL, automatically defined).

size

  size of the individual squares and font.

title

  character string, title of the plot

## Value

A heatmap of scaled mean expression, depicting markers in rows and cell populations in columns.

## Details

plot_marker_HM