shows the sequential processing steps that were performed on a Giotto object in a summarized format
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
#> python already initialized in this session
#> active environment : 'giotto_env'
#> python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#> "/usr/share/miniconda/envs/giotto_env/bin/python"
showProcessingSteps(g)
#> Warning: `showProcessingSteps()` was deprecated in GiottoClass 0.4.0.
#> ℹ Please use `objHistory()` instead.
#> ℹ objHistory with arg `summarized = TRUE` replaces this functionality
#> Processing steps:
#> 0_normalize
#> 1_subset
#> 2_filter
#> name info: tag tag
#> 3_feat_stats
#> 4_cell_stats
#> 5_hvf
#> name info: hvf HVFplot
#> 6_pca
#> 7_umap
#> 8_tsne
#> 9_nn_network
#> 10_cluster
#> name info: leiden_clus sNN.pca
#> 11_delaunay_spatial_network
#> name info: Delaunay_network
#> 12_spatial_network
#> name info: spatial_network
#> 13_create_metafeat
#> name info: cluster_metagene
#> 14_pca
#> name info: custom_pca
#> 15_umap
#> name info: custom_pca custom_umap
#> 16_nn_network
#> name info: custom_pca custom_NN
#> 17_cluster
#> name info: custom_leiden custom_NN
#> 18_spatial_deconvolution
#> name info: DWLS
#> 19_spatial_deconvolution
#> name info: DWLS
#> 20_spatial_deconvolution
#> name info: DWLS