update nanostring cosmx

drieslab · Sep 23, 2024 · 0430abd · 0430abd
1 parent 2fb78e6
commit 0430abd
Show file tree

Hide file tree

Showing 62 changed files with 142 additions and 172 deletions.
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/0-spatInSituPlotPoints.png b/vignettes/images/nanostring_cosmx_lung_cancer/0-spatInSituPlotPoints.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/1-spatPlot2D.png b/vignettes/images/nanostring_cosmx_lung_cancer/1-spatPlot2D.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/10-HVFplot.png b/vignettes/images/nanostring_cosmx_lung_cancer/10-HVFplot.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/10.1_gini_violin.png b/vignettes/images/nanostring_cosmx_lung_cancer/10.1_gini_violin.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/10.2_heatmap.png b/vignettes/images/nanostring_cosmx_lung_cancer/10.2_heatmap.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/10.3_gini_genes.png b/vignettes/images/nanostring_cosmx_lung_cancer/10.3_gini_genes.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/11-screePlot.png b/vignettes/images/nanostring_cosmx_lung_cancer/11-screePlot.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/11_anno_umap.png b/vignettes/images/nanostring_cosmx_lung_cancer/11_anno_umap.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/12-PCA.png b/vignettes/images/nanostring_cosmx_lung_cancer/12-PCA.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/12_spatdim_type.png b/vignettes/images/nanostring_cosmx_lung_cancer/12_spatdim_type.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/13-UMAP.png b/vignettes/images/nanostring_cosmx_lung_cancer/13-UMAP.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/13_insitu_type.png b/vignettes/images/nanostring_cosmx_lung_cancer/13_insitu_type.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/14-dimFeatPlot2D.png b/vignettes/images/nanostring_cosmx_lung_cancer/14-dimFeatPlot2D.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/14_ICF.png b/vignettes/images/nanostring_cosmx_lung_cancer/14_ICF.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/15-UMAP.png b/vignettes/images/nanostring_cosmx_lung_cancer/15-UMAP.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/16-spatDimPlot2D.png b/vignettes/images/nanostring_cosmx_lung_cancer/16-spatDimPlot2D.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/17-spatInSituPlotPoints.png b/vignettes/images/nanostring_cosmx_lung_cancer/17-spatInSituPlotPoints.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/18-spatInSituPlotPoints.png b/vignettes/images/nanostring_cosmx_lung_cancer/18-spatInSituPlotPoints.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/19-spatInSituPlotPoints.png b/vignettes/images/nanostring_cosmx_lung_cancer/19-spatInSituPlotPoints.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/1_inSituFeats.png b/vignettes/images/nanostring_cosmx_lung_cancer/1_inSituFeats.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/2-filterDistributions.png b/vignettes/images/nanostring_cosmx_lung_cancer/2-filterDistributions.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/20-spatInSituPlotPoints.png b/vignettes/images/nanostring_cosmx_lung_cancer/20-spatInSituPlotPoints.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/21-spatFeatPlot2D.png b/vignettes/images/nanostring_cosmx_lung_cancer/21-spatFeatPlot2D.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/22-violinPlot.png b/vignettes/images/nanostring_cosmx_lung_cancer/22-violinPlot.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/23-plotMetaDataHeatmap.png b/vignettes/images/nanostring_cosmx_lung_cancer/23-plotMetaDataHeatmap.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/24-dimFeatPlot2D.png b/vignettes/images/nanostring_cosmx_lung_cancer/24-dimFeatPlot2D.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/25-UMAP.png b/vignettes/images/nanostring_cosmx_lung_cancer/25-UMAP.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/26-spatDimPlot2D.png b/vignettes/images/nanostring_cosmx_lung_cancer/26-spatDimPlot2D.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/27-spatInSituPlotPoints.png b/vignettes/images/nanostring_cosmx_lung_cancer/27-spatInSituPlotPoints.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/28-spatInSituPlotPoints.png b/vignettes/images/nanostring_cosmx_lung_cancer/28-spatInSituPlotPoints.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/2_spatCentroids.png b/vignettes/images/nanostring_cosmx_lung_cancer/2_spatCentroids.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/3-filterDistributions.png b/vignettes/images/nanostring_cosmx_lung_cancer/3-filterDistributions.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/3.1_totalexpr.png b/vignettes/images/nanostring_cosmx_lung_cancer/3.1_totalexpr.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/3.2_totalnegprbe.png b/vignettes/images/nanostring_cosmx_lung_cancer/3.2_totalnegprbe.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/4-spatInSituPlotDensity.png b/vignettes/images/nanostring_cosmx_lung_cancer/4-spatInSituPlotDensity.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/4_inSituDens.png b/vignettes/images/nanostring_cosmx_lung_cancer/4_inSituDens.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/5-filterDistributions.png b/vignettes/images/nanostring_cosmx_lung_cancer/5-filterDistributions.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/5.1_rna_norm_total_hist.png b/vignettes/images/nanostring_cosmx_lung_cancer/5.1_rna_norm_total_hist.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/5.2_neg_norm_total_hist.png b/vignettes/images/nanostring_cosmx_lung_cancer/5.2_neg_norm_total_hist.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/5.3_color_centroids.png b/vignettes/images/nanostring_cosmx_lung_cancer/5.3_color_centroids.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/5.4_rna_color_polys.png b/vignettes/images/nanostring_cosmx_lung_cancer/5.4_rna_color_polys.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/5.5_neg_color_polys.png b/vignettes/images/nanostring_cosmx_lung_cancer/5.5_neg_color_polys.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/6-filterDistributions.png b/vignettes/images/nanostring_cosmx_lung_cancer/6-filterDistributions.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/6.1_pearson_HVF.png b/vignettes/images/nanostring_cosmx_lung_cancer/6.1_pearson_HVF.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/6.2_screeplot.png b/vignettes/images/nanostring_cosmx_lung_cancer/6.2_screeplot.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/6.3_PCA.png b/vignettes/images/nanostring_cosmx_lung_cancer/6.3_PCA.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/6.4_UMAP.png b/vignettes/images/nanostring_cosmx_lung_cancer/6.4_UMAP.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/6.5_UMAP_feats.png b/vignettes/images/nanostring_cosmx_lung_cancer/6.5_UMAP_feats.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/7-spatPlot2D.png b/vignettes/images/nanostring_cosmx_lung_cancer/7-spatPlot2D.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/7.1_UMAP_leiden.png b/vignettes/images/nanostring_cosmx_lung_cancer/7.1_UMAP_leiden.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/7.2_spatdim_leiden.png b/vignettes/images/nanostring_cosmx_lung_cancer/7.2_spatdim_leiden.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/7.3_spatinsitu_leiden.png b/vignettes/images/nanostring_cosmx_lung_cancer/7.3_spatinsitu_leiden.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/8-spatInSituPlotPoints.png b/vignettes/images/nanostring_cosmx_lung_cancer/8-spatInSituPlotPoints.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/8.1_smallfov_points.png b/vignettes/images/nanostring_cosmx_lung_cancer/8.1_smallfov_points.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/8.2_smallfov_poly.png b/vignettes/images/nanostring_cosmx_lung_cancer/8.2_smallfov_poly.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/8.3_smallfov_leiden.png b/vignettes/images/nanostring_cosmx_lung_cancer/8.3_smallfov_leiden.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/9-spatInSituPlotPoints.png b/vignettes/images/nanostring_cosmx_lung_cancer/9-spatInSituPlotPoints.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/9_binspect_genes.png b/vignettes/images/nanostring_cosmx_lung_cancer/9_binspect_genes.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/mat_comparison.png b/vignettes/images/nanostring_cosmx_lung_cancer/mat_comparison.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/preview_negprb.png b/vignettes/images/nanostring_cosmx_lung_cancer/preview_negprb.png
diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/values_diff.png b/vignettes/images/nanostring_cosmx_lung_cancer/values_diff.png
diff --git a/vignettes/nanostring_cosmx_lung_cancer.Rmd b/vignettes/nanostring_cosmx_lung_cancer.Rmd