Merge pull request #884 from josschavezf/suite

update mini_seqfish tutorial
drieslab · Feb 1, 2024 · 07d8c20 · 07d8c20
2 parents 1124129 + 9dae241
commit 07d8c20
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diff --git a/R/spatial_interaction_visuals.R b/R/spatial_interaction_visuals.R
@@ -2262,9 +2262,6 @@ plotRankSpatvsExpr = function(gobject,
     midpoint = gradient_midpoint,
     style = gradient_style,
     type = 'color',
-    type_default = list(
-      pal = c('blue', 'yellow', 'red')
-    ),
     guide = guide_legend(title = '')
   )
   pl = pl + ggplot2::scale_size_continuous(range = size_range, guide = "none")

diff --git a/vignettes/images/mini_seqfish/1-screePlot.png b/vignettes/images/mini_seqfish/1-screePlot.png
diff --git a/vignettes/images/mini_seqfish/11-spatDimPlot2D.png b/vignettes/images/mini_seqfish/11-spatDimPlot2D.png
diff --git a/vignettes/images/mini_seqfish/12-plotHeatmap.png b/vignettes/images/mini_seqfish/12-plotHeatmap.png
diff --git a/vignettes/images/mini_seqfish/14-plotStatDelaunayNetwork.png b/vignettes/images/mini_seqfish/14-plotStatDelaunayNetwork.png
diff --git a/vignettes/images/mini_seqfish/15-spatPlot2D.png b/vignettes/images/mini_seqfish/15-spatPlot2D.png
diff --git a/vignettes/images/mini_seqfish/16-spatPlot2D.png b/vignettes/images/mini_seqfish/16-spatPlot2D.png
diff --git a/vignettes/images/mini_seqfish/17-spatFeatPlot2D.png b/vignettes/images/mini_seqfish/17-spatFeatPlot2D.png
diff --git a/vignettes/images/mini_seqfish/18-spatFeatPlot2D.png b/vignettes/images/mini_seqfish/18-spatFeatPlot2D.png
diff --git a/vignettes/images/mini_seqfish/19-spatFeatPlot2D.png b/vignettes/images/mini_seqfish/19-spatFeatPlot2D.png
diff --git a/vignettes/images/mini_seqfish/2-PCA.png b/vignettes/images/mini_seqfish/2-PCA.png
diff --git a/vignettes/images/mini_seqfish/20-heatmSpatialCorFeats.png b/vignettes/images/mini_seqfish/20-heatmSpatialCorFeats.png
diff --git a/vignettes/images/mini_seqfish/21-rankSpatialCorGroups.png b/vignettes/images/mini_seqfish/21-rankSpatialCorGroups.png
diff --git a/vignettes/images/mini_seqfish/22-spatCellPlot2D.png b/vignettes/images/mini_seqfish/22-spatCellPlot2D.png
diff --git a/vignettes/images/mini_seqfish/25-cellProximityHeatmap.png b/vignettes/images/mini_seqfish/25-cellProximityHeatmap.png
diff --git a/vignettes/images/mini_seqfish/26-cellProximityNetwork.png b/vignettes/images/mini_seqfish/26-cellProximityNetwork.png
diff --git a/vignettes/images/mini_seqfish/27-cellProximityNetwork.png b/vignettes/images/mini_seqfish/27-cellProximityNetwork.png
diff --git a/vignettes/images/mini_seqfish/29-spatPlot2D.png b/vignettes/images/mini_seqfish/29-spatPlot2D.png
diff --git a/vignettes/images/mini_seqfish/3-UMAP.png b/vignettes/images/mini_seqfish/3-UMAP.png
diff --git a/vignettes/images/mini_seqfish/30-plotCellProximityFeats.png b/vignettes/images/mini_seqfish/30-plotCellProximityFeats.png
diff --git a/vignettes/images/mini_seqfish/30-plotCellProximityGenes.png b/vignettes/images/mini_seqfish/30-plotCellProximityGenes.png
diff --git a/vignettes/images/mini_seqfish/32-plotCCcomHeatmap.png b/vignettes/images/mini_seqfish/32-plotCCcomHeatmap.png
diff --git a/vignettes/images/mini_seqfish/33-plotCCcomDotplot.png b/vignettes/images/mini_seqfish/33-plotCCcomDotplot.png
diff --git a/vignettes/images/mini_seqfish/34-plotRankSpatvsExpr.png b/vignettes/images/mini_seqfish/34-plotRankSpatvsExpr.png
diff --git a/vignettes/images/mini_seqfish/4-tSNE.png b/vignettes/images/mini_seqfish/4-tSNE.png
diff --git a/vignettes/images/mini_seqfish/5-UMAP.png b/vignettes/images/mini_seqfish/5-UMAP.png
diff --git a/vignettes/images/mini_seqfish/6-spatDimPlot2D.png b/vignettes/images/mini_seqfish/6-spatDimPlot2D.png
diff --git a/vignettes/images/mini_seqfish/7-showClusterHeatmap.png b/vignettes/images/mini_seqfish/7-showClusterHeatmap.png
diff --git a/vignettes/images/mini_seqfish/9-violinPlot.png b/vignettes/images/mini_seqfish/9-violinPlot.png