Skip to contents

# Heatmap of scaled expression to compare two groups

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

`plot_marker_group_HM()` generates a heatmap of scaled mean marker expression for each cell population split by a grouping variable.

## Usage

    plot_marker_group_HM(
      fcd,
      expr_slot = "orig",
      marker_to_exclude = NULL,
      cluster_slot,
      cluster_var,
      group_var,
      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).

group_var

  string indicating variable name in cell_anno that should be used for subgrouping each cell population.

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 grouped by a grouping variable in columns.

## Details

plot_marker_group_HM