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