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drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
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Export and create Giotto Viewers #1012

Open 13954380607 opened 2 months ago

13954380607 commented 2 months ago

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('intissue', 'leidenclus'), 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 commented 2 months ago

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.