Compare gene expression between polygon areas#

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Last Updated: Mar 11, 2023

Description#

Compare gene expression between polygon areas

Usage#

comparePolygonExpression(
  gobject,
  polygon_name = "selections",
  spat_unit = "cell",
  feat_type = "rna",
  selected_feats = "top_genes",
  expression_values = "normalized",
  method = "scran",
  ...
)

Arguments#

gobject

A Giotto object

polygon_name

name of polygon selections

spat_unit

spatial unit (e.g. “cell”)

feat_type

feature type (e.g. “rna”, “dna”, “protein”)

selected_feats

vector of selected features to plot

expression_values

gene expression values to use (“normalized”, “scaled”, “custom”)

method

method to use to detect differentially expressed feats (“scran”, “gini”, “mast”)

...

Arguments passed to Heatmap

Value#

A ComplexHeatmap::Heatmap object