addCellIntMetadata

Creates an additional metadata column with information about interacting and non-interacting cell types of the selected cell-cell interaction.

addCellIntMetadata(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  spatial_network = "spatial_network",
  cluster_column,
  cell_interaction,
  name = "select_int",
  return_gobject = TRUE
)

Arguments

gobject

giotto object

spat_unit

spatial unit

feat_type

feature type

spatial_network

name of spatial network to use

cluster_column

column of cell types

cell_interaction

cell-cell interaction to use

name

name for the new metadata column

return_gobject

return an updated giotto object

Value

Giotto object

Details

This function will create an additional metadata column which selects interacting cell types for a specific cell-cell interaction. For example, if you want to color interacting astrocytes and oligodendrocytes it will create a new metadata column with the values "select_astrocytes", "select_oligodendrocytes", "other_astrocytes", "other_oligodendroyctes" and "other". Where "other" is all other cell types found within the selected cell type column.

Examples

g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/bin/python3"
#> Warning: Some of Giotto's expected python module(s) were not found:
#> pandas, igraph, leidenalg, community, networkx, sklearn
#> (This is fine if python-based functions are not needed)
#> 
#> ** Python path used: "/usr/bin/python3"

addCellIntMetadata(g,
    cluster_column = "leiden_clus",
    cell_interaction = "custom_leiden"
)
#> An object of class giotto 
#> >Active spat_unit:  cell 
#> >Active feat_type:  rna 
#> dimensions    : 634, 624 (features, cells)
#> [SUBCELLULAR INFO]
#> polygons      : cell 
#> [AGGREGATE INFO]
#> expression -----------------------
#>   [cell][rna] raw normalized scaled
#> spatial locations ----------------
#>   [cell] raw
#> spatial networks -----------------
#>   [cell] Delaunay_network spatial_network
#> spatial enrichments --------------
#>   [cell][rna] cluster_metagene DWLS
#> dim reduction --------------------
#>   [cell][rna] pca custom_pca umap custom_umap tsne
#> nearest neighbor networks --------
#>   [cell][rna] sNN.pca custom_NN
#> attached images ------------------
#> images      : alignment image 
#> 
#> 
#> Use objHistory() to see steps and params used