Files in kueckelj/SPATA2
A Toolbox for Spatial Gene Expression Analysis
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/.gitignore
R/Geoms.R
R/S4-documentation.R
R/S4-generic-functions.R
R/add.R
R/adj-aZ.R
R/b.R
R/c.R
R/check.R
R/create.R
R/d.R
R/data.R
R/deprecated_a-i.R
R/deprecated_j-z.R
R/dev.R
R/documentation-dummies.R
R/e.R
R/f.R
R/g.R
R/getA-G.R
R/getH-M.R
R/getN-Z.R
R/h.R
R/i.R
R/imported-functions.R
R/initiateSpataObject.R
R/j.R
R/l.R
R/m.R
R/n.R
R/o.R
R/p.R
R/package-dependencies.R
R/plotA-D.R
R/plotF-G.R
R/plotH-M.R
R/plotN-S.R
R/plotSurface.R
R/plotT-Z.R
R/plot_.R
R/r-objects.R
R/r.R
R/runA-Z.R
R/s.R
R/setA-Z.R
R/t.R
R/u.R
R/unused.R
R/v.R
R/w.R
README.md
SPATA2.Rproj
data/clustering.rda
data/cnv_ref.rda
data/cnv_regions_df.rda
data/dea.rda
data/gene_pos_df.rda
data/gsdf.rda
data/image_annotations.rda
data/sc_deconvolution.rda
data/scale_factors.rda
data/snn_clustering.rda
data/spatial_segmentations.rda
data/spatial_trajectories.rda
data/visium_coords.rda
data/visium_coords_lowres.rda
docs/404.html
docs/articles/cc-image-annotation-screening.html
docs/articles/cc-image-annotation-screening_files/figure-html/add_polygon-1.png
docs/articles/cc-image-annotation-screening_files/figure-html/load-session-1.png
docs/articles/cc-image-annotation-screening_files/figure-html/load-session-2.png
docs/articles/cc-image-annotation-screening_files/figure-html/n_bins_circle-1.png
docs/articles/cc-image-annotation-screening_files/figure-html/unnamed-chunk-10-1.png
docs/articles/cc-image-annotation-screening_files/figure-html/unnamed-chunk-10-2.png
docs/articles/cc-image-annotation-screening_files/figure-html/unnamed-chunk-11-1.png
docs/articles/cc-image-annotation-screening_files/figure-html/unnamed-chunk-13-1.png
docs/articles/cc-image-annotation-screening_files/figure-html/unnamed-chunk-14-1.png
docs/articles/cc-image-annotation-screening_files/figure-html/unnamed-chunk-3-1.png
docs/articles/cc-image-annotation-screening_files/figure-html/unnamed-chunk-7-1.png
docs/articles/cc-image-annotation-screening_files/figure-html/unnamed-chunk-9-1.png
docs/articles/cc-image-annotation-screening_files/figure-html/unnamed-chunk-9-2.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies.html
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/example genes-1.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/lineplots-1.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/the-models-1.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-10-1.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-12-1.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-13-1.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-13-2.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-13-3.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-13-4.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-14-1.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-14-2.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-14-3.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-14-4.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-16-1.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-19-1.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-19-2.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-21-1.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-21-2.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-23-1.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-23-2.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-23-3.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-23-4.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-25-1.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-25-2.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-6-1.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-6-2.png
docs/articles/cc-model-fitting-in-spatial-transcriptomic-studies_files/figure-html/unnamed-chunk-8-1.png
docs/articles/cc-spatial-measures.html
docs/articles/cc-spatial-measures_files/figure-html/unnamed-chunk-13-1.png
docs/articles/cc-spatial-measures_files/figure-html/unnamed-chunk-13-2.png
docs/articles/cc-spatial-measures_files/figure-html/unnamed-chunk-14-1.png
docs/articles/cc-spatial-measures_files/figure-html/unnamed-chunk-14-2.png
docs/articles/cc-spatial-measures_files/figure-html/unnamed-chunk-15-1.png
docs/articles/cc-spatial-measures_files/figure-html/unnamed-chunk-15-2.png
docs/articles/cc-spatial-measures_files/figure-html/unnamed-chunk-16-1.png
docs/articles/cc-spatial-measures_files/figure-html/unnamed-chunk-24-1.png
docs/articles/cc-spatial-measures_files/figure-html/unnamed-chunk-3-1.png
docs/articles/cc-spatial-measures_files/figure-html/unnamed-chunk-3-2.png
docs/articles/cc-spatial-measures_files/figure-html/unnamed-chunk-5-1.png
docs/articles/cc-spatial-measures_files/figure-html/unnamed-chunk-5-2.png
docs/articles/cc-spatial-measures_files/figure-html/unnamed-chunk-8-1.png
docs/articles/cc-spatial-segmentation-vs-image-annotations.html
docs/articles/cc-spatial-segmentation-vs-image-annotations_files/figure-html/images-1.png
docs/articles/cc-spatial-segmentation-vs-image-annotations_files/figure-html/images-2.png
docs/articles/cc-spatial-segmentation-vs-image-annotations_files/figure-html/unnamed-chunk-11-1.png
docs/articles/cc-spatial-segmentation-vs-image-annotations_files/figure-html/unnamed-chunk-13-1.png
docs/articles/cc-spatial-segmentation-vs-image-annotations_files/figure-html/unnamed-chunk-15-1.png
docs/articles/cc-spatial-segmentation-vs-image-annotations_files/figure-html/unnamed-chunk-5-1.png
docs/articles/cc-spatial-segmentation-vs-image-annotations_files/figure-html/unnamed-chunk-5-2.png
docs/articles/cc-spatial-segmentation-vs-image-annotations_files/figure-html/unnamed-chunk-7-1.png
docs/articles/cc-spatial-segmentation-vs-image-annotations_files/figure-html/unnamed-chunk-8-1.png
docs/articles/cc-spatial-trajectory-screening.html
docs/articles/cc-spatial-trajectory-screening_files/figure-html/unnamed-chunk-10-1.png
docs/articles/cc-spatial-trajectory-screening_files/figure-html/unnamed-chunk-12-1.png
docs/articles/cc-spatial-trajectory-screening_files/figure-html/unnamed-chunk-14-1.png
docs/articles/cc-spatial-trajectory-screening_files/figure-html/unnamed-chunk-14-2.png
docs/articles/cc-spatial-trajectory-screening_files/figure-html/unnamed-chunk-15-1.png
docs/articles/cc-spatial-trajectory-screening_files/figure-html/unnamed-chunk-16-1.png
docs/articles/cc-spatial-trajectory-screening_files/figure-html/unnamed-chunk-16-2.png
docs/articles/cc-spatial-trajectory-screening_files/figure-html/unnamed-chunk-17-1.png
docs/articles/cc-spatial-trajectory-screening_files/figure-html/unnamed-chunk-3-1.png
docs/articles/cc-spatial-trajectory-screening_files/figure-html/unnamed-chunk-3-2.png
docs/articles/cc-spatial-trajectory-screening_files/figure-html/unnamed-chunk-4-1.png
docs/articles/cc-spatial-trajectory-screening_files/figure-html/unnamed-chunk-4-2.png
docs/articles/cc-spatial-trajectory-screening_files/figure-html/unnamed-chunk-7-1.png
docs/articles/cc-spatial-trajectory-screening_files/figure-html/unnamed-chunk-7-2.png
docs/articles/cc-spatial-trajectory-screening_files/figure-html/unnamed-chunk-9-1.png
docs/articles/images/annotate_image_zooming.JPG
docs/articles/images/annotate_image_zooming2.JPG
docs/articles/images/createSpatialSegmentation_create_segm_var.JPG
docs/articles/images/createSpatialSegmentation_enter_segm_var.JPG
docs/articles/images/createSpatialSegmentation_interface.JPG
docs/articles/images/createSpatialSegmentation_new_segm_var.JPG
docs/articles/images/create_image_annotations_screenshot.JPG
docs/articles/images/create_segmentation_screenshot.JPG
docs/articles/images/create_spat_trajectories_highlighted.JPG
docs/articles/images/create_spat_trajectories_interface_traj.JPG
docs/articles/images/drawing.JPG
docs/articles/images/drawn_enter_tags_and_name.JPG
docs/articles/images/genes-and-gene-sets-fig-1.png
docs/articles/images/interactive-plotting-hypoxic-area.png
docs/articles/images/interactive-plotting-metrn_high.png
docs/articles/images/interactive_segmentation_1.png
docs/articles/images/interactive_segmentation_2.JPG
docs/articles/images/interactive_segmentation_3.JPG
docs/articles/images/interactive_segmentation_4.JPG
docs/articles/images/interactive_segmentation_5.JPG
docs/articles/images/interactive_segmentation_6.JPG
docs/articles/images/spata_data_healthy_brain_tab.JPG
docs/articles/images/spata_data_pathological_brain_tab.JPG
docs/articles/index.html
docs/articles/markdown-styles.css
docs/articles/spata-v2-autoencoder.html
docs/articles/spata-v2-autoencoder_files/figure-html/example-surface-1.png
docs/articles/spata-v2-autoencoder_files/figure-html/example-surface-2.png
docs/articles/spata-v2-autoencoder_files/figure-html/example-surface2-1.png
docs/articles/spata-v2-autoencoder_files/figure-html/example-surface2-2.png
docs/articles/spata-v2-autoencoder_files/figure-html/example_genes-correlation-1.png
docs/articles/spata-v2-autoencoder_files/figure-html/example_genes-distribution-1.png
docs/articles/spata-v2-autoencoder_files/figure-html/example_genes-distribution-2.png
docs/articles/spata-v2-autoencoder_files/figure-html/example_genes-surface3-1.png
docs/articles/spata-v2-autoencoder_files/figure-html/example_genes-surface3-2.png
docs/articles/spata-v2-autoencoder_files/figure-html/runAutoencoderAssessment()-invis-1.png
docs/articles/spata-v2-clustering.html
docs/articles/spata-v2-clustering_files/figure-html/unnamed-chunk-2-1.png
docs/articles/spata-v2-clustering_files/figure-html/unnamed-chunk-6-1.png
docs/articles/spata-v2-clustering_files/figure-html/unnamed-chunk-9-1.png
docs/articles/spata-v2-cnv-analysis.html
docs/articles/spata-v2-cnv-analysis_files/figure-html/unnamed-chunk-10-1.png
docs/articles/spata-v2-cnv-analysis_files/figure-html/unnamed-chunk-11-1.png
docs/articles/spata-v2-cnv-analysis_files/figure-html/unnamed-chunk-11-2.png
docs/articles/spata-v2-cnv-analysis_files/figure-html/unnamed-chunk-12-1.png
docs/articles/spata-v2-cnv-analysis_files/figure-html/unnamed-chunk-12-2.png
docs/articles/spata-v2-cnv-analysis_files/figure-html/unnamed-chunk-12-3.png
docs/articles/spata-v2-cnv-analysis_files/figure-html/unnamed-chunk-12-4.png
docs/articles/spata-v2-cnv-analysis_files/figure-html/unnamed-chunk-3-1.png
docs/articles/spata-v2-cnv-analysis_files/figure-html/unnamed-chunk-3-2.png
docs/articles/spata-v2-cnv-analysis_files/figure-html/unnamed-chunk-8-1.png
docs/articles/spata-v2-cnv-analysis_files/figure-html/unnamed-chunk-9-1.png
docs/articles/spata-v2-dea.html
docs/articles/spata-v2-dea_files/figure-html/unnamed-chunk-12-1.png
docs/articles/spata-v2-dea_files/figure-html/unnamed-chunk-13-1.png
docs/articles/spata-v2-dea_files/figure-html/unnamed-chunk-14-1.png
docs/articles/spata-v2-dea_files/figure-html/unnamed-chunk-16-1.png
docs/articles/spata-v2-dea_files/figure-html/unnamed-chunk-17-1.png
docs/articles/spata-v2-dea_files/figure-html/unnamed-chunk-18-1.png
docs/articles/spata-v2-dea_files/figure-html/unnamed-chunk-2-1.png
docs/articles/spata-v2-dea_files/figure-html/unnamed-chunk-2-2.png
docs/articles/spata-v2-dea_files/figure-html/unnamed-chunk-4-1.png
docs/articles/spata-v2-dea_files/figure-html/unnamed-chunk-4-2.png
docs/articles/spata-v2-genes-gene-sets-and-features.html
docs/articles/spata-v2-genes-gene-sets-and-features_files/figure-html/renameGroups()-1.png
docs/articles/spata-v2-gsea.html
docs/articles/spata-v2-gsea_files/figure-html/unnamed-chunk-2-1.png
docs/articles/spata-v2-gsea_files/figure-html/unnamed-chunk-2-2.png
docs/articles/spata-v2-gsea_files/figure-html/unnamed-chunk-7-1.png
docs/articles/spata-v2-gsea_files/figure-html/unnamed-chunk-8-1.png
docs/articles/spata-v2-image-annotation-screening.html
docs/articles/spata-v2-image-annotation-screening_files/figure-html/unnamed-chunk-10-1.png
docs/articles/spata-v2-image-annotation-screening_files/figure-html/unnamed-chunk-13-1.png
docs/articles/spata-v2-image-annotation-screening_files/figure-html/unnamed-chunk-14-1.png
docs/articles/spata-v2-image-annotation-screening_files/figure-html/unnamed-chunk-14-2.png
docs/articles/spata-v2-image-annotation-screening_files/figure-html/unnamed-chunk-14-3.png
docs/articles/spata-v2-image-annotation-screening_files/figure-html/unnamed-chunk-14-4.png
docs/articles/spata-v2-image-annotation-screening_files/figure-html/unnamed-chunk-15-1.png
docs/articles/spata-v2-image-annotation-screening_files/figure-html/unnamed-chunk-19-1.png
docs/articles/spata-v2-image-annotation-screening_files/figure-html/unnamed-chunk-20-1.png
docs/articles/spata-v2-image-annotation-screening_files/figure-html/unnamed-chunk-3-1.png
docs/articles/spata-v2-image-annotation-screening_files/figure-html/unnamed-chunk-3-2.png
docs/articles/spata-v2-image-annotation-screening_files/figure-html/unnamed-chunk-4-1.png
docs/articles/spata-v2-image-annotation-screening_files/figure-html/unnamed-chunk-4-2.png
docs/articles/spata-v2-image-annotation-screening_files/figure-html/unnamed-chunk-5-1.png
docs/articles/spata-v2-image-annotation-screening_files/figure-html/unnamed-chunk-5-2.png
docs/articles/spata-v2-image-annotation-screening_files/figure-html/unnamed-chunk-6-1.png
docs/articles/spata-v2-image-annotation-screening_files/figure-html/unnamed-chunk-7-1.png
docs/articles/spata-v2-image-annotation-screening_files/figure-html/volcano_IAS-1.png
docs/articles/spata-v2-image-annotations.html
docs/articles/spata-v2-image-annotations_files/figure-html/ggpLayer2-1.png
docs/articles/spata-v2-image-annotations_files/figure-html/unnamed-chunk-10-1.png
docs/articles/spata-v2-image-annotations_files/figure-html/unnamed-chunk-11-1.png
docs/articles/spata-v2-image-annotations_files/figure-html/unnamed-chunk-11-2.png
docs/articles/spata-v2-image-annotations_files/figure-html/unnamed-chunk-12-1.png
docs/articles/spata-v2-image-annotations_files/figure-html/unnamed-chunk-12-2.png
docs/articles/spata-v2-image-annotations_files/figure-html/unnamed-chunk-13-1.png
docs/articles/spata-v2-image-annotations_files/figure-html/unnamed-chunk-4-1.png
docs/articles/spata-v2-image-annotations_files/figure-html/using_tags-1.png
docs/articles/spata-v2-image-annotations_files/figure-html/using_tags-2.png
docs/articles/spata-v2-image-handling.html
docs/articles/spata-v2-image-handling_files/figure-html/unnamed-chunk-10-1.png
docs/articles/spata-v2-image-handling_files/figure-html/unnamed-chunk-10-2.png
docs/articles/spata-v2-image-handling_files/figure-html/unnamed-chunk-12-1.png
docs/articles/spata-v2-image-handling_files/figure-html/unnamed-chunk-13-1.png
docs/articles/spata-v2-image-handling_files/figure-html/unnamed-chunk-14-1.png
docs/articles/spata-v2-image-handling_files/figure-html/unnamed-chunk-17-1.png
docs/articles/spata-v2-image-handling_files/figure-html/unnamed-chunk-19-1.png
docs/articles/spata-v2-image-handling_files/figure-html/unnamed-chunk-19-2.png
docs/articles/spata-v2-image-handling_files/figure-html/unnamed-chunk-5-1.png
docs/articles/spata-v2-image-handling_files/figure-html/unnamed-chunk-7-1.png
docs/articles/spata-v2-image-handling_files/figure-html/unnamed-chunk-7-2.png
docs/articles/spata-v2-installation.html
docs/articles/spata-v2-object-initiation-and-manipulation.html
docs/articles/spata-v2-platform-compatibility.html
docs/articles/spata-v2-plotting-misc.html
docs/articles/spata-v2-plotting-misc_files/figure-html/unnamed-chunk-2-1.png
docs/articles/spata-v2-plotting-misc_files/figure-html/unnamed-chunk-3-1.png
docs/articles/spata-v2-plotting-misc_files/figure-html/unnamed-chunk-4-1.png
docs/articles/spata-v2-plotting-misc_files/figure-html/unnamed-chunk-5-1.png
docs/articles/spata-v2-plotting-misc_files/figure-html/unnamed-chunk-6-1.png
docs/articles/spata-v2-plotting-misc_files/figure-html/unnamed-chunk-7-1.png
docs/articles/spata-v2-plotting-misc_files/figure-html/unnamed-chunk-8-1.png
docs/articles/spata-v2-plotting-misc_files/figure-html/unnamed-chunk-9-1.png
docs/articles/spata-v2-plotting-surface.html
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-10-1.png
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-10-2.png
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-14-1.png
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-14-2.png
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-15-1.png
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-3-1.png
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-3-2.png
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-4-1.png
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-4-2.png
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-5-1.png
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-5-2.png
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-6-1.png
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-6-2.png
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-7-1.png
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-7-2.png
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-8-1.png
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-8-2.png
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-9-1.png
docs/articles/spata-v2-plotting-surface_files/figure-html/unnamed-chunk-9-2.png
docs/articles/spata-v2-scd.html
docs/articles/spata-v2-scd_files/figure-html/unnamed-chunk-11-1.png
docs/articles/spata-v2-scd_files/figure-html/unnamed-chunk-11-2.png
docs/articles/spata-v2-scd_files/figure-html/unnamed-chunk-2-1.png
docs/articles/spata-v2-scd_files/figure-html/unnamed-chunk-2-2.png
docs/articles/spata-v2-scd_files/figure-html/unnamed-chunk-5-1.png
docs/articles/spata-v2-scd_files/figure-html/unnamed-chunk-6-1.png
docs/articles/spata-v2-scd_files/figure-html/unnamed-chunk-7-1.png
docs/articles/spata-v2-scd_files/figure-html/unnamed-chunk-8-1.png
docs/articles/spata-v2-scd_files/figure-html/unnamed-chunk-8-2.png
docs/articles/spata-v2-spata-data.html
docs/articles/spata-v2-spatial-segmentation.html
docs/articles/spata-v2-spatial-segmentation_files/figure-html/unnamed-chunk-15-1.png
docs/articles/spata-v2-spatial-segmentation_files/figure-html/unnamed-chunk-17-1.png
docs/articles/spata-v2-spatial-segmentation_files/figure-html/unnamed-chunk-17-2.png
docs/articles/spata-v2-spatial-segmentation_files/figure-html/unnamed-chunk-18-1.png
docs/articles/spata-v2-spatial-segmentation_files/figure-html/unnamed-chunk-18-2.png
docs/articles/spata-v2-spatial-segmentation_files/figure-html/unnamed-chunk-2-1.png
docs/articles/spata-v2-spatial-segmentation_files/figure-html/unnamed-chunk-2-2.png
docs/articles/spata-v2-spatial-segmentation_files/figure-html/unnamed-chunk-20-1.png
docs/articles/spata-v2-spatial-segmentation_files/figure-html/unnamed-chunk-21-1.png
docs/articles/spata-v2-spatial-trajectories.html
docs/articles/spata-v2-spatial-trajectories_files/figure-html/unnamed-chunk-10-1.png
docs/articles/spata-v2-spatial-trajectories_files/figure-html/unnamed-chunk-11-1.png
docs/articles/spata-v2-spatial-trajectories_files/figure-html/unnamed-chunk-11-2.png
docs/articles/spata-v2-spatial-trajectories_files/figure-html/unnamed-chunk-11-3.png
docs/articles/spata-v2-spatial-trajectories_files/figure-html/unnamed-chunk-11-4.png
docs/articles/spata-v2-spatial-trajectories_files/figure-html/unnamed-chunk-2-1.png
docs/articles/spata-v2-spatial-trajectories_files/figure-html/unnamed-chunk-2-2.png
docs/articles/spata-v2-spatial-trajectories_files/figure-html/unnamed-chunk-8-1.png
docs/articles/spata-v2-spatial-trajectories_files/figure-html/unnamed-chunk-9-1.png
docs/articles/spata-v2-spatial-trajectory-screening.html
docs/articles/spata-v2-spatial-trajectory-screening_files/figure-html/unnamed-chunk-10-1.png
docs/articles/spata-v2-spatial-trajectory-screening_files/figure-html/unnamed-chunk-11-1.png
docs/articles/spata-v2-spatial-trajectory-screening_files/figure-html/unnamed-chunk-13-1.png
docs/articles/spata-v2-spatial-trajectory-screening_files/figure-html/unnamed-chunk-2-1.png
docs/articles/spata-v2-spatial-trajectory-screening_files/figure-html/unnamed-chunk-2-2.png
docs/articles/spata-v2-spatial-trajectory-screening_files/figure-html/unnamed-chunk-3-1.png
docs/articles/spata-v2-spatial-trajectory-screening_files/figure-html/unnamed-chunk-8-1.png
docs/articles/spata-v2-spatial-trajectory-screening_files/figure-html/unnamed-chunk-9-1.png
docs/articles/spata-v2-spatial-trajectory-screening_files/figure-html/unnamed-chunk-9-2.png
docs/articles/spata-v2-spatial-trajectory-screening_files/figure-html/unnamed-chunk-9-3.png
docs/articles/spata-v2-subsetting.html
docs/articles/spata-v2-subsetting_files/figure-html/unnamed-chunk-2-1.png
docs/articles/spata-v2-subsetting_files/figure-html/unnamed-chunk-3-1.png
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/images/Logo.png
docs/images/autoencoder.png
docs/images/cnv-analysis.png
docs/images/main-header.svg
docs/images/spatial-segmentation.png
docs/images/sub-header-de-analysis.png
docs/images/sub-header-ias.png
docs/images/sub-header-img-anns.png
docs/images/sub-header-spat-traj.png
docs/images/sub-header-sts.png
docs/images/sub-header-visualization.png
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/GeomPointFixed.html
docs/reference/GeomSegmentFixed.html
docs/reference/GeomTextFixed.html
docs/reference/HistologyImage-class.html
docs/reference/HistologyImaging-class.html
docs/reference/ImageAnnotation-class.html
docs/reference/ImageAnnotationScreening-class.html
docs/reference/SpatialMethod-class.html
docs/reference/SpatialSegment-class.html
docs/reference/SpatialSegmentation-class.html
docs/reference/SpatialTrajectory-class.html
docs/reference/SpatialTrajectoryScreening-class.html
docs/reference/Trajectory-class.html
docs/reference/across.html
docs/reference/addAutoencoderSetUp.html
docs/reference/addExpressionMatrix.html
docs/reference/addFeatures.html
docs/reference/addGeneFeatures.html
docs/reference/addGeneMetaData.html
docs/reference/addGeneSet.html
docs/reference/addImageDir.html
docs/reference/addPointsBase.html
docs/reference/addSpCorCluster.html
docs/reference/add_dbscan_variable.html
docs/reference/add_models.html
docs/reference/add_outline_variable.html
docs/reference/adjustDirectoryInstructions.html
docs/reference/adjustGeneSetDf.html
docs/reference/alignImageAnnotation.html
docs/reference/allColorpalettes.html
docs/reference/all_bcsp_distances.html
docs/reference/all_color_palettes.html
docs/reference/append_polygon_df.html
docs/reference/are_all_area_or_dist.html
docs/reference/argument_dummy.html
docs/reference/arrange_as_polygon.html
docs/reference/asGiotto.html
docs/reference/asHistologyImage.html
docs/reference/asHistologyImaging.html
docs/reference/asSPATA2.html
docs/reference/asSeurat.html
docs/reference/asSingleCellExperiment.html
docs/reference/asSpatialTrajectory.html
docs/reference/asSummarizedExperiment.html
docs/reference/asVisiumV1.html
docs/reference/as_SPATA2_dist.html
docs/reference/as_unit.html
docs/reference/attachUnit.html
docs/reference/average_genes.html
docs/reference/bin_by_angle.html
docs/reference/bin_by_expansion.html
docs/reference/binwidth_dummy.html
docs/reference/buffer_area.html
docs/reference/cds_dummy.html
docs/reference/check_all_barcodes.html
docs/reference/check_assign.html
docs/reference/check_atdf.html
docs/reference/check_availability.html
docs/reference/check_color_to.html
docs/reference/check_compiled_trajectory_df.html
docs/reference/check_coordinate_variables.html
docs/reference/check_coords_df.html
docs/reference/check_customized_trends.html
docs/reference/check_dea_df.html
docs/reference/check_display.html
docs/reference/check_feature_df.html
docs/reference/check_features.html
docs/reference/check_gene_sets.html
docs/reference/check_genes.html
docs/reference/check_method.html
docs/reference/check_monocle_input.html
docs/reference/check_monocle_packages.html
docs/reference/check_object.html
docs/reference/check_pattern.html
docs/reference/check_pt.html
docs/reference/check_sample.html
docs/reference/check_saving.html
docs/reference/check_segment.html
docs/reference/check_slot_coordinates.html
docs/reference/check_smooth.html
docs/reference/check_spata_df.html
docs/reference/check_stdf.html
docs/reference/check_summarized_trajectory_df.html
docs/reference/check_to.html
docs/reference/check_trajectory.html
docs/reference/check_trajectory_binwidth.html
docs/reference/check_uniform_genes.html
docs/reference/check_variables.html
docs/reference/checkpoint.html
docs/reference/close_area_df.html
docs/reference/clrp.html
docs/reference/clusterSpCorResults.html
docs/reference/clustering.html
docs/reference/cnv_ref.html
docs/reference/cnv_regions_df.html
docs/reference/color_vector.html
docs/reference/computeCnvByChrArm.html
docs/reference/computeGeneMetaData.html
docs/reference/compute_angle_between_two_points.html
docs/reference/compute_distance.html
docs/reference/containsCNV.html
docs/reference/containsHistologyImaging.html
docs/reference/containsImage.html
docs/reference/containsPixelScaleFactor.html
docs/reference/countImageAnnotationTags.html
docs/reference/createHistologyImaging.html
docs/reference/createImageAnnotations.html
docs/reference/createSegmentation.html
docs/reference/createSpatialSegmentation.html
docs/reference/createSpatialTrajectories.html
docs/reference/create_model_df.html
docs/reference/cropSpataObject.html
docs/reference/data_counts-class.html
docs/reference/dea.html
docs/reference/default_instructions-class.html
docs/reference/dim_red-class.html
docs/reference/discardExpressionMatrix.html
docs/reference/discardFeatures.html
docs/reference/discardGeneFeatures.html
docs/reference/discardGeneSets.html
docs/reference/discardGenes.html
docs/reference/discardImageAnnotations.html
docs/reference/downloadPubExample.html
docs/reference/downloadRawData.html
docs/reference/downloadSpataObject.html
docs/reference/dropped_df_dummy.html
docs/reference/examineClusterResults.html
docs/reference/exchangeImage.html
docs/reference/export.html
docs/reference/extract_unit.html
docs/reference/extract_value.html
docs/reference/filterDeaDf.html
docs/reference/findMonocleClusters.html
docs/reference/findNearestNeighbourClusters.html
docs/reference/findSeuratClusters.html
docs/reference/flexible_call_dummy.html
docs/reference/flipAll.html
docs/reference/flipCoords.html
docs/reference/flip_coords_df.html
docs/reference/gene_pos_df.html
docs/reference/gene_set_path.html
docs/reference/geom_point_fixed.html
docs/reference/geom_segment_fixed.html
docs/reference/geom_text_fixed.html
docs/reference/getActiveMatrixName.html
docs/reference/getAutoencoderAssessment.html
docs/reference/getAutoencoderSetUp.html
docs/reference/getBarcodeSpotDistance.html
docs/reference/getBarcodeSpotDistances.html
docs/reference/getBarcodes.html
docs/reference/getBarcodesInPolygon.html
docs/reference/getCCD.html
docs/reference/getChrRegionsDf.html
docs/reference/getCnvFeatureNames.html
docs/reference/getCnvGenesDf.html
docs/reference/getCnvResults.html
docs/reference/getCoordsCenter.html
docs/reference/getCoordsDf.html
docs/reference/getCoordsRange.html
docs/reference/getDeaLfcName.html
docs/reference/getDeaOverview.html
docs/reference/getDeaResultsDf.html
docs/reference/getDefaultInstructions.html
docs/reference/getDimRedDf.html
docs/reference/getExpressionMatrixNames.html
docs/reference/getFeatureDf.html
docs/reference/getFeatureNames.html
docs/reference/getFeatureValues.html
docs/reference/getFeatureVariables.html
docs/reference/getFromSeurat.html
docs/reference/getGeneCounts.html
docs/reference/getGeneDistMtr.html
docs/reference/getGeneFeatureNames.html
docs/reference/getGeneMetaData.html
docs/reference/getGenePosDf.html
docs/reference/getGeneSetDf.html
docs/reference/getGeneSetOverview.html
docs/reference/getGeneSets.html
docs/reference/getGenes.html
docs/reference/getGroupNames.html
docs/reference/getGroupingOptions.html
docs/reference/getGseaDf.html
docs/reference/getGseaResults.html
docs/reference/getIasBinAreas.html
docs/reference/getIasDf.html
docs/reference/getIasExpansion.html
docs/reference/getImage.html
docs/reference/getImageAnnotation.html
docs/reference/getImageAnnotations.html
docs/reference/getImageCenter.html
docs/reference/getImageDf.html
docs/reference/getImageDims.html
docs/reference/getImageDirLowres.html
docs/reference/getImageInfo.html
docs/reference/getImageObject.html
docs/reference/getImageOrigin.html
docs/reference/getImageRaster.html
docs/reference/getImageSectionsByBarcode.html
docs/reference/getImgAnnArea.html
docs/reference/getImgAnnBarcodes.html
docs/reference/getImgAnnCenter.html
docs/reference/getImgAnnCenterBcsp.html
docs/reference/getImgAnnIds.html
docs/reference/getImgAnnOutlineDf.html
docs/reference/getImgAnnRange.html
docs/reference/getImgAnnSf.html
docs/reference/getImgAnnSummaryDf.html
docs/reference/getImgAnnTags.html
docs/reference/getInitiationInfo.html
docs/reference/getMatrix.html
docs/reference/getModelEvaluationDf.html
docs/reference/getPixelDf.html
docs/reference/getPixelScaleFactor.html
docs/reference/getPrResults.html
docs/reference/getProjectionDf.html
docs/reference/getResultsDf.html
docs/reference/getResultsVec.html
docs/reference/getSampleAreaSize.html
docs/reference/getSampleName.html
docs/reference/getSegmentNames.html
docs/reference/getSegmentationNames.html
docs/reference/getSignatureEnrichment.html
docs/reference/getSmrdResultsDf.html
docs/reference/getSpCorCluster.html
docs/reference/getSpCorResults.html
docs/reference/getSpataDf.html
docs/reference/getSpataDir.html
docs/reference/getSpatialMethod.html
docs/reference/getSpatialTrajectory.html
docs/reference/getSpatialTrajectoryIds.html
docs/reference/getStsDf.html
docs/reference/getTissueOutlineDf.html
docs/reference/getTrajectoryDf.html
docs/reference/getTrajectoryIds.html
docs/reference/getTrajectoryLength.html
docs/reference/getTrajectoryNames.html
docs/reference/getTrajectoryScreeningDf.html
docs/reference/getTrajectorySegmentDf.html
docs/reference/getVariableNames.html
docs/reference/get_img_ann_helper.html
docs/reference/ggpInit.html
docs/reference/ggpLayerAxesClean.html
docs/reference/ggpLayerAxesSI.html
docs/reference/ggpLayerColorGroupScale.html
docs/reference/ggpLayerEncirclingIAS.html
docs/reference/ggpLayerFrame.html
docs/reference/ggpLayerFrameByCoords.html
docs/reference/ggpLayerGroupOutline.html
docs/reference/ggpLayerHorizonIAS.html
docs/reference/ggpLayerImage.html
docs/reference/ggpLayerImgAnnOutline.html
docs/reference/ggpLayerImgAnnPointer.html
docs/reference/ggpLayerImgAnnRect.html
docs/reference/ggpLayerLineplotAid.html
docs/reference/ggpLayerRect.html
docs/reference/ggpLayerScaleBarSI.html
docs/reference/ggpLayerThemeCoords.html
docs/reference/ggpLayerTissueOutline.html
docs/reference/ggpLayerTrajectories.html
docs/reference/ggpLayerZoom.html
docs/reference/ggpLayer_dummy.html
docs/reference/ggplot_dummy.html
docs/reference/ggplot_family.html
docs/reference/gradientToModelIAS.html
docs/reference/gsdf.html
docs/reference/hlpr_add_barcode_suffix.html
docs/reference/hlpr_add_old_coords.html
docs/reference/hlpr_adjust_legend_size.html
docs/reference/hlpr_assign_arguments.html
docs/reference/hlpr_breaks.html
docs/reference/hlpr_compare_samples.html
docs/reference/hlpr_dist_mtr_to_df.html
docs/reference/hlpr_gene_set_name.html
docs/reference/hlpr_geom_trajectory_fit.html
docs/reference/hlpr_image_add_on.html
docs/reference/hlpr_join_with_color_by.html
docs/reference/hlpr_labs_add_on.html
docs/reference/hlpr_normalize_imap.html
docs/reference/hlpr_normalize_vctr.html
docs/reference/hlpr_one_distinct.html
docs/reference/hlpr_process_spatial_correlation_cluster.html
docs/reference/hlpr_rank_trajectory_trends.html
docs/reference/hlpr_save_spata_object.html
docs/reference/hlpr_scatterplot.html
docs/reference/hlpr_smooth.html
docs/reference/hlpr_smooth_shiny.html
docs/reference/hlpr_subset_across.html
docs/reference/hlpr_summarize_trajectory_df.html
docs/reference/hlpr_vector_projection.html
docs/reference/hlpr_widen_trajectory_df.html
docs/reference/imageAnnotationScreening.html
docs/reference/imageAnnotationToSegmentation.html
docs/reference/image_annotations.html
docs/reference/image_dummy.html
docs/reference/include_tissue_outline.html
docs/reference/index.html
docs/reference/inferSingleCellGradient.html
docs/reference/initiateSpataObject_10X.html
docs/reference/initiateSpataObject_CountMtr.html
docs/reference/initiateSpataObject_Empty.html
docs/reference/initiateSpataObject_Examples.html
docs/reference/initiateSpataObject_ExprMtr.html
docs/reference/intersect_polygons.html
docs/reference/is_area.html
docs/reference/is_dist.html
docs/reference/is_unit_area.html
docs/reference/is_unit_dist.html
docs/reference/joinWith.html
docs/reference/joinWithPca.html
docs/reference/legendBottom.html
docs/reference/loadGSDF.html
docs/reference/loadGeneSetDf.html
docs/reference/loadImageLowres.html
docs/reference/loadSpataObject.html
docs/reference/makeContent.resizingSegmentsGrob.html
docs/reference/makeContent.resizingTextGrob.html
docs/reference/mapImageAnnotationTags.html
docs/reference/mergeGroups.html
docs/reference/method_hclust.html
docs/reference/moduleAddGeneSetsServer.html
docs/reference/moduleAddGeneSetsUI.html
docs/reference/moduleSurfacePlotServer.html
docs/reference/moduleSurfacePlotUI.html
docs/reference/nBarcodes.html
docs/reference/nCounts.html
docs/reference/nGenes.html
docs/reference/nImageAnnotations.html
docs/reference/nSpatialTrajectories.html
docs/reference/normalize.html
docs/reference/object_dummy.html
docs/reference/pb_dummy.html
docs/reference/pheatmap.html
docs/reference/plotAutoencoderAssessment.html
docs/reference/plotAutoencoderResults.html
docs/reference/plotBarchart.html
docs/reference/plotBoxplot.html
docs/reference/plotClockplot.html
docs/reference/plotCnvHeatmap.html
docs/reference/plotCnvLineplot.html
docs/reference/plotDeaDotPlot.html
docs/reference/plotDeaGeneCount.html
docs/reference/plotDeaHeatmap.html
docs/reference/plotDeaPvalues.html
docs/reference/plotDeaSummary.html
docs/reference/plotDeaVolcano.html
docs/reference/plotDendrogram.html
docs/reference/plotFourStates.html
docs/reference/plotGeneDendrogram.html
docs/reference/plotGseaDotPlot.html
docs/reference/plotIasBarplot.html
docs/reference/plotIasEvaluation.html
docs/reference/plotIasHeatmap.html
docs/reference/plotIasLineplot.html
docs/reference/plotIasLineplotFitted.html
docs/reference/plotIasRidgeplot.html
docs/reference/plotImage.html
docs/reference/plotImageAnnotations.html
docs/reference/plotImageGgplot.html
docs/reference/plotImagesGgplot.html
docs/reference/plotMosaicplot.html
docs/reference/plotOverview.html
docs/reference/plotPcaVariation.html
docs/reference/plotPseudotime.html
docs/reference/plotRiverplot.html
docs/reference/plotScatterplot.html
docs/reference/plotSpatialTrajectories.html
docs/reference/plotStatisticsInteractive.html
docs/reference/plotSurface.html
docs/reference/plotSurfaceAverage.html
docs/reference/plotSurfaceBase.html
docs/reference/plotSurfaceComparison.html
docs/reference/plotSurfaceIAS.html
docs/reference/plotSurfaceQuantiles.html
docs/reference/plotSurfaceSC.html
docs/reference/plotTrajectoryBarplot.html
docs/reference/plotTrajectoryEvaluation.html
docs/reference/plotTrajectoryHeatmap.html
docs/reference/plotTrajectoryLineplot.html
docs/reference/plotTrajectoryLineplotFitted.html
docs/reference/plotUmap.html
docs/reference/plotVolcano.html
docs/reference/plot_screening_evaluation.html
docs/reference/plot_type_dummy.html
docs/reference/printAutoencoderSummary.html
docs/reference/printDeaOverview.html
docs/reference/printDefaultInstructions.html
docs/reference/printGeneSetOverview.html
docs/reference/print_family.html
docs/reference/process_expand_input.html
docs/reference/process_ranges.html
docs/reference/process_seurat_object.html
docs/reference/project_on_trajectory.html
docs/reference/project_on_vector.html
docs/reference/reduce_vec.html
docs/reference/relateToImageAnnotation.html
docs/reference/relevelGroups.html
docs/reference/removeAnnotation.html
docs/reference/renameFeatures.html
docs/reference/renameGroups.html
docs/reference/renameImgAnn.html
docs/reference/resetImageJustification.html
docs/reference/resizingSegmentsGrob.html
docs/reference/resizingTextGrob.html
docs/reference/rotateAll.html
docs/reference/rotate_coords_df.html
docs/reference/runAutoencoderAssessment.html
docs/reference/runAutoencoderDenoising.html
docs/reference/runBayesSpaceClustering.html
docs/reference/runCnvAnalysis.html
docs/reference/runDEA.html
docs/reference/runGSEA.html
docs/reference/runPca.html
docs/reference/runSeuratClustering.html
docs/reference/runSparkx.html
docs/reference/runSpatialCorrelationAnalysis.html
docs/reference/runTsne.html
docs/reference/runUmap.html
docs/reference/sample_name.html
docs/reference/saveGeneSetDf.html
docs/reference/saveSpataObject.html
docs/reference/sc_deconvolution.html
docs/reference/scaleAll.html
docs/reference/scale_color_add_on.html
docs/reference/scale_coords_df.html
docs/reference/scale_factors.html
docs/reference/section_dummy.html
docs/reference/setActiveExpressionMatrix.html
docs/reference/setAutoencoderAssessment.html
docs/reference/setBarcodes.html
docs/reference/setCnvResults.html
docs/reference/setCoordsDf.html
docs/reference/setCountMatrix.html
docs/reference/setDefault.html
docs/reference/setDefaultGrouping.html
docs/reference/setDefaultInstructions.html
docs/reference/setDefaultTrajectory.html
docs/reference/setFeatureDf.html
docs/reference/setGeneSetDf.html
docs/reference/setImageAnnotation.html
docs/reference/setImageDirLowres.html
docs/reference/setImageObject.html
docs/reference/setImageOrigin.html
docs/reference/setInitiationInfo.html
docs/reference/setOutlineVarName.html
docs/reference/setPcaDf.html
docs/reference/setPixelScaleFactor.html
docs/reference/setPrResults.html
docs/reference/setSpCorResults.html
docs/reference/setSpataDir.html
docs/reference/setTissueOutline.html
docs/reference/setTrajectory.html
docs/reference/set_dummy.html
docs/reference/seurat_object_dummy.html
docs/reference/showColors.html
docs/reference/showModels.html
docs/reference/smoothSpatially.html
docs/reference/spata2-class.html
docs/reference/spatialTrajectoryScreening.html
docs/reference/spatial_segmentations.html
docs/reference/spatial_trajectories.html
docs/reference/spatial_trajectory-class.html
docs/reference/subsetByBarcodes.html
docs/reference/subsetByGenes.html
docs/reference/summarizeIAS.html
docs/reference/summarize_formulas.html
docs/reference/tab_surface_plots_app.html
docs/reference/tab_surface_plots_return.html
docs/reference/theme_lineplot_gradient.html
docs/reference/transfer_slot_content.html
docs/reference/transformSeuratToSpata.html
docs/reference/transformSpataToCDS.html
docs/reference/transformSpataToSeurat.html
docs/reference/transform_area_si_to_pixel.html
docs/reference/transform_dist_si_to_pixel.html
docs/reference/transform_pixel_to_area_si.html
docs/reference/transform_pixel_to_dist_si.html
docs/reference/transform_pixel_to_si.html
docs/reference/translate_shape_string.html
docs/reference/updateSpataObject.html
docs/reference/update_dummy.html
docs/reference/validActivationFunctions.html
docs/reference/validation.html
docs/reference/variable.html
docs/reference/variable_num.html
docs/reference/variables_num.html
docs/reference/visium_coords.html
docs/reference/vselect.html
docs/sitemap.xml
docs/styles.css
man/GeomPointFixed.Rd
man/GeomSegmentFixed.Rd
man/GeomTextFixed.Rd
man/HistologyImage-class.Rd
man/HistologyImaging-class.Rd
man/ImageAnnotation-class.Rd
man/ImageAnnotationScreening-class.Rd
man/SpatialMethod-class.Rd
man/SpatialSegment-class.Rd
man/SpatialSegmentation-class.Rd
man/SpatialTrajectory-class.Rd
man/SpatialTrajectoryScreening-class.Rd
man/Trajectory-class.Rd
man/Visium-class.Rd
man/across.Rd
man/addAutoencoderSetUp.Rd
man/addExpressionMatrix.Rd
man/addFeatures.Rd
man/addGeneFeatures.Rd
man/addGeneMetaData.Rd
man/addGeneSet.Rd
man/addImageDir.Rd
man/addPointsBase.Rd
man/addSpCorCluster.Rd
man/add_dbscan_variable.Rd
man/add_models.Rd
man/add_outline_variable.Rd
man/adjustDirectoryInstructions.Rd
man/adjustGeneSetDf.Rd
man/alignImageAnnotation.Rd
man/allColorpalettes.Rd
man/all_bcsp_distances.Rd
man/all_color_palettes.Rd
man/append_polygon_df.Rd
man/are_all_area_or_dist.Rd
man/argument_dummy.Rd
man/arrange_as_polygon.Rd
man/asGiotto.Rd
man/asHistologyImage.Rd
man/asHistologyImaging.Rd
man/asSPATA2.Rd
man/asSeurat.Rd
man/asSingleCellExperiment.Rd
man/asSpatialTrajectory.Rd
man/asSummarizedExperiment.Rd
man/asVisiumV1.Rd
man/as_SPATA2_dist.Rd
man/as_unit.Rd
man/attachUnit.Rd
man/average_genes.Rd
man/barcodesToImageAnnotation.Rd
man/bin_by_angle.Rd
man/bin_by_expansion.Rd
man/binwidth_dummy.Rd
man/buffer_area.Rd
man/cds_dummy.Rd
man/check_all_barcodes.Rd
man/check_assign.Rd
man/check_atdf.Rd
man/check_availability.Rd
man/check_color_to.Rd
man/check_compiled_trajectory_df.Rd
man/check_coordinate_variables.Rd
man/check_coords_df.Rd
man/check_customized_trends.Rd
man/check_dea_df.Rd
man/check_display.Rd
man/check_feature_df.Rd
man/check_features.Rd
man/check_gene_sets.Rd
man/check_genes.Rd
man/check_method.Rd
man/check_monocle_input.Rd
man/check_monocle_packages.Rd
man/check_object.Rd
man/check_pattern.Rd
man/check_pt.Rd
man/check_sample.Rd
man/check_saving.Rd
man/check_segment.Rd
man/check_slot_coordinates.Rd
man/check_smooth.Rd
man/check_spata_df.Rd
man/check_stdf.Rd
man/check_summarized_trajectory_df.Rd
man/check_to.Rd
man/check_trajectory.Rd
man/check_trajectory_binwidth.Rd
man/check_uniform_genes.Rd
man/check_variables.Rd
man/checkpoint.Rd
man/close_area_df.Rd
man/clrp.Rd
man/clusterSpCorResults.Rd
man/clustering.Rd
man/cnv_ref.Rd
man/cnv_regions_df.Rd
man/color_vector.Rd
man/computeCnvByChrArm.Rd
man/computeGeneMetaData.Rd
man/compute_angle_between_two_points.Rd
man/compute_distance.Rd
man/containsCNV.Rd
man/containsHistologyImaging.Rd
man/containsImage.Rd
man/containsPixelScaleFactor.Rd
man/countImageAnnotationTags.Rd
man/createHistologyImaging.Rd
man/createImageAnnotations.Rd
man/createSegmentation.Rd
man/createSpatialSegmentation.Rd
man/createSpatialTrajectories.Rd
man/create_model_df.Rd
man/cropSpataObject.Rd
man/currentSpata2Version.Rd
man/data_counts-class.Rd
man/dea.Rd
man/default_instructions-class.Rd
man/deprecatedInfo.Rd
man/dim_red-class.Rd
man/discardExpressionMatrix.Rd
man/discardFeatures.Rd
man/discardGeneFeatures.Rd
man/discardGeneSets.Rd
man/discardGenes.Rd
man/discardImageAnnotations.Rd
man/downloadPubExample.Rd
man/downloadRawData.Rd
man/downloadSpataObject.Rd
man/dropped_df_dummy.Rd
man/examineClusterResults.Rd
man/exchangeImage.Rd
man/export.Rd
man/extract_unit.Rd
man/extract_value.Rd
man/filterDeaDf.Rd
man/findMonocleClusters.Rd
man/findNearestNeighbourClusters.Rd
man/findSeuratClusters.Rd
man/flexible_call_dummy.Rd
man/flipAll.Rd
man/flipCoords.Rd
man/flip_coords_df.Rd
man/gene_pos_df.Rd
man/gene_set_path.Rd
man/geom_point_fixed.Rd
man/geom_segment_fixed.Rd
man/geom_text_fixed.Rd
man/getActiveMatrixName.Rd
man/getAutoencoderAssessment.Rd
man/getAutoencoderSetUp.Rd
man/getBarcodeSpotDistance.Rd
man/getBarcodeSpotDistances.Rd
man/getBarcodes.Rd
man/getBarcodesInPolygon.Rd
man/getCCD.Rd
man/getChrRegionsDf.Rd
man/getCnvFeatureNames.Rd
man/getCnvGenesDf.Rd
man/getCnvResults.Rd
man/getCoordsCenter.Rd
man/getCoordsDf.Rd
man/getCoordsRange.Rd
man/getDeaLfcName.Rd
man/getDeaOverview.Rd
man/getDeaResultsDf.Rd
man/getDefaultInstructions.Rd
man/getDimRedDf.Rd
man/getExpressionMatrixNames.Rd
man/getFeatureDf.Rd
man/getFeatureNames.Rd
man/getFeatureValues.Rd
man/getFeatureVariables.Rd
man/getFromSeurat.Rd
man/getGeneCounts.Rd
man/getGeneDistMtr.Rd
man/getGeneFeatureNames.Rd
man/getGeneMetaData.Rd
man/getGenePosDf.Rd
man/getGeneSetDf.Rd
man/getGeneSetOverview.Rd
man/getGeneSets.Rd
man/getGenes.Rd
man/getGroupNames.Rd
man/getGroupingOptions.Rd
man/getGseaDf.Rd
man/getGseaResults.Rd
man/getIasBinAreas.Rd
man/getIasDf.Rd
man/getIasExpansion.Rd
man/getImage.Rd
man/getImageAnnotation.Rd
man/getImageAnnotations.Rd
man/getImageCenter.Rd
man/getImageDf.Rd
man/getImageDims.Rd
man/getImageDirLowres.Rd
man/getImageInfo.Rd
man/getImageObject.Rd
man/getImageOrigin.Rd
man/getImageRaster.Rd
man/getImageSectionsByBarcode.Rd
man/getImgAnnArea.Rd
man/getImgAnnBarcodes.Rd
man/getImgAnnCenter.Rd
man/getImgAnnCenterBcsp.Rd
man/getImgAnnIds.Rd
man/getImgAnnOutlineDf.Rd
man/getImgAnnRange.Rd
man/getImgAnnSf.Rd
man/getImgAnnSummaryDf.Rd
man/getImgAnnTags.Rd
man/getInitiationInfo.Rd
man/getMatrix.Rd
man/getModelEvaluationDf.Rd
man/getPixelDf.Rd
man/getPixelScaleFactor.Rd
man/getPrResults.Rd
man/getProjectionDf.Rd
man/getResultsDf.Rd
man/getResultsVec.Rd
man/getSampleAreaSize.Rd
man/getSampleName.Rd
man/getSegmentNames.Rd
man/getSegmentationNames.Rd
man/getSignatureEnrichment.Rd
man/getSmrdResultsDf.Rd
man/getSpCorCluster.Rd
man/getSpCorResults.Rd
man/getSpataDf.Rd
man/getSpataDir.Rd
man/getSpatialMethod.Rd
man/getSpatialTrajectory.Rd
man/getSpatialTrajectoryIds.Rd
man/getStsDf.Rd
man/getTissueOutlineDf.Rd
man/getTrajectoryDf.Rd
man/getTrajectoryIds.Rd
man/getTrajectoryLength.Rd
man/getTrajectoryNames.Rd
man/getTrajectoryScreeningDf.Rd
man/getTrajectorySegmentDf.Rd
man/getVariableNames.Rd
man/get_img_ann_helper.Rd
man/ggpInit.Rd
man/ggpLayerAxesClean.Rd
man/ggpLayerAxesSI.Rd
man/ggpLayerColorGroupScale.Rd
man/ggpLayerEncirclingIAS.Rd
man/ggpLayerFrame.Rd
man/ggpLayerFrameByCoords.Rd
man/ggpLayerGroupOutline.Rd
man/ggpLayerHorizonIAS.Rd
man/ggpLayerImage.Rd
man/ggpLayerImgAnnOutline.Rd
man/ggpLayerImgAnnPointer.Rd
man/ggpLayerImgAnnRect.Rd
man/ggpLayerLineplotAid.Rd
man/ggpLayerRect.Rd
man/ggpLayerScaleBarSI.Rd
man/ggpLayerThemeCoords.Rd
man/ggpLayerTissueOutline.Rd
man/ggpLayerTrajectories.Rd
man/ggpLayerZoom.Rd
man/ggpLayer_dummy.Rd
man/ggplot_dummy.Rd
man/ggplot_family.Rd
man/gradientToModelIAS.Rd
man/gsdf.Rd
man/hlpr_add_barcode_suffix.Rd
man/hlpr_add_old_coords.Rd
man/hlpr_adjust_legend_size.Rd
man/hlpr_assign_arguments.Rd
man/hlpr_breaks.Rd
man/hlpr_compare_samples.Rd
man/hlpr_dist_mtr_to_df.Rd
man/hlpr_gene_set_name.Rd
man/hlpr_geom_trajectory_fit.Rd
man/hlpr_image_add_on.Rd
man/hlpr_join_with_color_by.Rd
man/hlpr_labs_add_on.Rd
man/hlpr_normalize_imap.Rd
man/hlpr_normalize_vctr.Rd
man/hlpr_one_distinct.Rd
man/hlpr_process_spatial_correlation_cluster.Rd
man/hlpr_rank_trajectory_trends.Rd
man/hlpr_save_spata_object.Rd
man/hlpr_scatterplot.Rd
man/hlpr_smooth.Rd
man/hlpr_smooth_shiny.Rd
man/hlpr_subset_across.Rd
man/hlpr_summarize_trajectory_df.Rd
man/hlpr_vector_projection.Rd
man/hlpr_widen_trajectory_df.Rd
man/identifyTissueOutline.Rd
man/identifyTissueSections.Rd
man/imageAnnotationScreening.Rd
man/imageAnnotationToSegmentation.Rd
man/image_annotations.Rd
man/image_dummy.Rd
man/include_tissue_outline.Rd
man/inferSingleCellGradient.Rd
man/initiateSpataObject_10X.Rd
man/initiateSpataObject_CountMtr.Rd
man/initiateSpataObject_Empty.Rd
man/initiateSpataObject_Examples.Rd
man/initiateSpataObject_ExprMtr.Rd
man/intersect_polygons.Rd
man/is_area.Rd
man/is_dist.Rd
man/is_unit_area.Rd
man/is_unit_dist.Rd
man/joinWith.Rd
man/joinWithPca.Rd
man/legendBottom.Rd
man/loadGSDF.Rd
man/loadGeneSetDf.Rd
man/loadImageLowres.Rd
man/loadSpataObject.Rd
man/makeContent.resizingSegmentsGrob.Rd
man/makeContent.resizingTextGrob.Rd
man/mapImageAnnotationTags.Rd
man/mergeGroups.Rd
man/mergeTissueSections.Rd
man/method_hclust.Rd
man/moduleAddGeneSetsServer.Rd
man/moduleAddGeneSetsUI.Rd
man/moduleSurfacePlotServer.Rd
man/moduleSurfacePlotUI.Rd
man/nBarcodes.Rd
man/nCounts.Rd
man/nGenes.Rd
man/nImageAnnotations.Rd
man/nSpatialTrajectories.Rd
man/normalize.Rd
man/object_dummy.Rd
man/pb_dummy.Rd
man/pheatmap.Rd
man/plotAutoencoderAssessment.Rd
man/plotAutoencoderResults.Rd
man/plotBarchart.Rd
man/plotBoxplot.Rd
man/plotClockplot.Rd
man/plotCnvHeatmap.Rd
man/plotCnvLineplot.Rd
man/plotDeaDotPlot.Rd
man/plotDeaGeneCount.Rd
man/plotDeaHeatmap.Rd
man/plotDeaPvalues.Rd
man/plotDeaSummary.Rd
man/plotDeaVolcano.Rd
man/plotDendrogram.Rd
man/plotFourStates.Rd
man/plotGeneDendrogram.Rd
man/plotGseaDotPlot.Rd
man/plotIasBarplot.Rd
man/plotIasEvaluation.Rd
man/plotIasHeatmap.Rd
man/plotIasLineplot.Rd
man/plotIasLineplotFitted.Rd
man/plotIasRidgeplot.Rd
man/plotImage.Rd
man/plotImageAnnotations.Rd
man/plotImageGgplot.Rd
man/plotImagesGgplot.Rd
man/plotMosaicplot.Rd
man/plotOverview.Rd
man/plotPcaVariation.Rd
man/plotPseudotime.Rd
man/plotRiverplot.Rd
man/plotScatterplot.Rd
man/plotSpatialTrajectories.Rd
man/plotStatisticsInteractive.Rd
man/plotSurface.Rd
man/plotSurfaceAverage.Rd
man/plotSurfaceBase.Rd
man/plotSurfaceComparison.Rd
man/plotSurfaceIAS.Rd
man/plotSurfaceQuantiles.Rd
man/plotSurfaceSC.Rd
man/plotTrajectoryBarplot.Rd
man/plotTrajectoryEvaluation.Rd
man/plotTrajectoryHeatmap.Rd
man/plotTrajectoryLineplot.Rd
man/plotTrajectoryLineplotFitted.Rd
man/plotUmap.Rd
man/plotVolcano.Rd
man/plot_screening_evaluation.Rd
man/plot_type_dummy.Rd
man/printAutoencoderSummary.Rd
man/printDeaOverview.Rd
man/printDefaultInstructions.Rd
man/printGeneSetOverview.Rd
man/print_family.Rd
man/process_expand_input.Rd
man/process_ranges.Rd
man/process_seurat_object.Rd
man/project_on_trajectory.Rd
man/project_on_vector.Rd
man/reduce_vec.Rd
man/relateToImageAnnotation.Rd
man/relevelGroups.Rd
man/removeAnnotation.Rd
man/renameFeatures.Rd
man/renameGroups.Rd
man/renameImgAnn.Rd
man/resetImageJustification.Rd
man/resizingSegmentsGrob.Rd
man/resizingTextGrob.Rd
man/rotateAll.Rd
man/rotate_coords_df.Rd
man/runAutoencoderAssessment.Rd
man/runAutoencoderDenoising.Rd
man/runBayesSpaceClustering.Rd
man/runCnvAnalysis.Rd
man/runDEA.Rd
man/runGSEA.Rd
man/runPca.Rd
man/runSeuratClustering.Rd
man/runSparkx.Rd
man/runSpatialCorrelationAnalysis.Rd
man/runTsne.Rd
man/runUmap.Rd
man/sample_name.Rd
man/saveGeneSetDf.Rd
man/saveSpataObject.Rd
man/sc_deconvolution.Rd
man/scaleAll.Rd
man/scale_color_add_on.Rd
man/scale_coords_df.Rd
man/scale_factors.Rd
man/section_dummy.Rd
man/setActiveExpressionMatrix.Rd
man/setAutoencoderAssessment.Rd
man/setBarcodes.Rd
man/setCCD.Rd
man/setCnvResults.Rd
man/setCoordsDf.Rd
man/setCountMatrix.Rd
man/setDefault.Rd
man/setDefaultGrouping.Rd
man/setDefaultInstructions.Rd
man/setDefaultTrajectory.Rd
man/setFeatureDf.Rd
man/setGeneSetDf.Rd
man/setImageAnnotation.Rd
man/setImageDirLowres.Rd
man/setImageObject.Rd
man/setImageOrigin.Rd
man/setInitiationInfo.Rd
man/setOutlineVarName.Rd
man/setPcaDf.Rd
man/setPixelScaleFactor.Rd
man/setPrResults.Rd
man/setSpCorResults.Rd
man/setSpataDir.Rd
man/setSpatialMethod.Rd
man/setSpatialMethodInfo.Rd
man/setSpatialMethodSlot.Rd
man/setTissueOutline.Rd
man/setTrajectory.Rd
man/set_dummy.Rd
man/seurat_object_dummy.Rd
man/showColors.Rd
man/showModels.Rd
man/smoothSpatially.Rd
man/spata2-class.Rd
man/spatialTrajectoryScreening.Rd
man/spatial_segmentations.Rd
man/spatial_trajectories.Rd
man/spatial_trajectory-class.Rd
man/subsetByBarcodes.Rd
man/subsetByGenes.Rd
man/summarizeIAS.Rd
man/summarize_formulas.Rd
man/tab_surface_plots_app.Rd
man/tab_surface_plots_return.Rd
man/theme_lineplot_gradient.Rd
man/tissueOutlineIdentified.Rd
man/transfer_slot_content.Rd
man/transformSeuratToSpata.Rd
man/transformSpataToCDS.Rd
man/transformSpataToSeurat.Rd
man/transform_area_si_to_pixel.Rd
man/transform_dist_si_to_pixel.Rd
man/transform_pixel_to_area_si.Rd
man/transform_pixel_to_dist_si.Rd
man/transform_pixel_to_si.Rd
man/translate_shape_string.Rd
man/updateSpataObject.Rd
man/update_dummy.Rd
man/validActivationFunctions.Rd
man/validation.Rd
man/variable.Rd
man/variable_num.Rd
man/variables_num.Rd
man/visium_coords.Rd
man/vselect.Rd
