Export and create Giotto Viewers

[13954380607]

combineMetadata(visium_kidney)

select annotations, reductions and expression values to view in Giotto Viewer

viewer_folder = paste0(results_folder, '/', 'mouse_visium_kidney_viewer')

exportGiottoViewer(gobject = visium_kidney,
output_directory = viewer_folder,
factor_annotations = c('in_tissue',
'leiden_clus'),
numeric_annotations = c('nr_feats'),
dim_reductions = c('tsne', 'umap'),
dim_reduction_names = c('tsne', 'umap'),
expression_values = 'scaled',
expression_rounding = 2,
overwrite_dir = T)

Error:
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'j' in selecting a method for function '[': could not find function "."

[josschavezf]

Hi @13954380607, unfortunately, the Giotto viewer is no longer supported. We are working on creating new visualization tools. In the meantime, you can still generate the dimension reductions and spatial plots using the spatPlot, spatFeatPlot, plotUMAP, and plotPCA functions.