This function generates a heatmap of average marker expressions, grouped by a specified metadata column. The heatmap allows customization of clustering distance, color palette, font size, and scaling method.
Usage
plotAvgHeatmap(
data,
group_column,
only_relevant_markers = FALSE,
clustering_distance = "euclidean",
colors = rev((grDevices::colorRampPalette(RColorBrewer::brewer.pal(n = 11,
"RdYlBu")))(100)),
fontsize = 8,
scale = "column",
cluster_rows = FALSE,
na.rm = TRUE
)Arguments
- data
An object of class
CygnusObjectcontaining an expression matrix and metadata.- group_column
Character string specifying the metadata column to group by.
- only_relevant_markers
Logical value indicating whether only relevant markers should be plotted.
- clustering_distance
Character string specifying the distance metric for clustering columns. Default is "euclidean".
- colors
A color palette to use for the heatmap. Default is a reversed "RdYlBu" palette from RColorBrewer.
- fontsize
Numeric value specifying the font size for heatmap text. Default is 8.
- scale
Character string specifying whether the data should be scaled by 'row', 'column', or 'none'. Default is 'column'.
- cluster_rows
Logical value indicating whether to cluster rows in the heatmap. Default is FALSE.
- na.rm
Logical value indicating whether to remove NA values before calculating averages. Default is TRUE.