Heatmap of average expression values per group

Usage

DoClusteredHeatmap(
  object,
  features = NULL,
  assay = "RNA",
  layer = "data",
  group.by = "seurat_clusters",
  max_zed = 3,
  y_text_size = 10,
  scale_rows = TRUE,
  plot_dendro = FALSE,
  dot.scale = 5,
  cluster_cols = TRUE,
  cluster_rows = TRUE,
  viridis_option = "B",
  viridis_direction = 1
)

Arguments

object: Seurat object
features: Which features to plot
assay: Which assay to get expression values from
layer: Which layer to pull the assay data from
group.by: Which metadata layer to group cells by
max_zed: Cutoff for maximum z-scores (absolute value)
y_text_size: Size of text on y axis (features)
scale_rows: Whether to scale the expression per row
plot_dendro: Whether to plot accompanying x-axis and y-axis dendrograms
dot.scale: Value by which to scale the dots in DotPlot
cluster_cols: Whether to cluster the columns
cluster_rows: Whether to cluster the rows
viridis_option: The viridis color scale to use
viridis_direction: The direction of the viridis color scale

Value

Returns a patchwork object of a heatmap and dendrogram if specified

Details

Plots the average expression value of the specified genes/features for each group in the Seurat object, optionally using hierarchical clustering for prettier visualization