createHeatmap_DT: createHeatmap_DT
In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

createHeatmap_DT

R Documentation

createHeatmap_DT

Description

creates order for clusters

Usage

createHeatmap_DT(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  feats,
  genes = NULL,
  cluster_column = NULL,
  cluster_order = c("size", "correlation", "custom"),
  cluster_custom_order = NULL,
  cluster_cor_method = "pearson",
  cluster_hclust_method = "ward.D",
  feat_order = c("correlation", "custom"),
  gene_order = NULL,
  feat_custom_order = NULL,
  gene_custom_order = NULL,
  feat_cor_method = "pearson",
  gene_cor_method = NULL,
  feat_hclust_method = "complete",
  gene_hclust_method = NULL
)

Arguments

`gobject`	giotto object
`spat_unit`	spatial unit (e.g. "cell")
`feat_type`	feature type (e.g. "rna", "dna", "protein")
`expression_values`	expression values to use (e.g. "normalized", "scaled", "custom")
`feats`	features to use
`genes`	deprecated, use feats
`cluster_column`	name of column to use for clusters (e.g. "leiden_clus")
`cluster_order`	method to determine cluster order (e.g. "size", "correlation", "custom")
`cluster_custom_order`	custom order for clusters
`cluster_cor_method`	method for cluster correlation, default to "pearson"
`cluster_hclust_method`	method for hierarchical clustering of clusters, default to "ward.D"
`feat_order`	method to determine features order (e.g. "correlation", "custom")
`gene_order`	deprecated, use feat_order in the future
`feat_custom_order`	custom order for features
`gene_custom_order`	deprecated, use feat_custom_order in the future
`feat_cor_method`	method for features correlation, default to "pearson"
`gene_cor_method`	deprecated, use feat_cor_method in the future
`feat_hclust_method`	method for hierarchical clustering of features, default to "complete"
`gene_hclust_method`	deprecated, use feat_hclust_method in the future