S4 giotto Class — giotto-class • Giotto

Framework of giotto object to store and work with spatial expression data

Slots

raw_exprs: raw expression counts
norm_expr: normalized expression counts
norm_scaled_expr: normalized and scaled expression counts
custom_expr: custom normalized counts
spatial_locs: spatial location coordinates for cells
cell_metadata: metadata for cells
gene_metadata: metadata for genes
cell_ID: unique cell IDs
gene_ID: unique gene IDs
spatial_network: spatial network in data.table/data.frame format
spatial_grid: spatial grid in data.table/data.frame format
spatial_enrichment: slot to save spatial enrichment-like results
dimension_reduction: slot to save dimension reduction coordinates
nn_network: nearest neighbor network in igraph format
images: slot to store giotto images
parameters: slot to save parameters that have been used
instructions: slot for global function instructions
offset_file: offset file used to stitch together image fields
OS_platform: Operating System to run Giotto analysis on