Merge branch 'suite_dev' into mrd_xenium

drieslab · Jul 31, 2024 · 2f40060 · 2f40060
2 parents 2b8c5f7 + 047d0b0
commit 2f40060
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Showing 20 changed files with 1,321 additions and 84 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -114,12 +114,14 @@ Suggests:
     SummarizedExperiment,
     tidygraph,
     trendsceek,
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    rmarkdown
 Remotes:
     drieslab/GiottoUtils,
     drieslab/GiottoClass,
     drieslab/GiottoVisuals
 Collate:
+    'ONTraC_wrapper.R'
     'auxiliary_giotto.R'
     'cell_segmentation.R'
     'clustering.R'

diff --git a/NAMESPACE b/NAMESPACE
@@ -238,6 +238,7 @@ export(getGEFtxCoords)
 export(getGiottoImage)
 export(getMultiomics)
 export(getNearestNetwork)
+export(getONTraCv1Input)
 export(getPolygonInfo)
 export(getRainbowColors)
 export(getSpatialEnrichment)
@@ -274,6 +275,7 @@ export(jackstrawPlot)
 export(joinGiottoObjects)
 export(loadGiotto)
 export(loadHMRF)
+export(loadOntraCResults)
 export(makePseudoVisium)
 export(makeSignMatrixDWLS)
 export(makeSignMatrixDWLSfromMatrix)
@@ -293,8 +295,10 @@ export(pieCellTypesFromEnrichment)
 export(plotCCcomDotplot)
 export(plotCCcomHeatmap)
 export(plotCPF)
+export(plotCTCompositionInNicheCluster)
 export(plotCellProximityFeatSpot)
 export(plotCellProximityFeats)
+export(plotCellTypeNTScore)
 export(plotCellTypesFromEnrichment)
 export(plotCombineCCcom)
 export(plotCombineCellCellCommunication)
@@ -309,6 +313,7 @@ export(plotInteractive3D)
 export(plotInteractivePolygons)
 export(plotMetaDataCellsHeatmap)
 export(plotMetaDataHeatmap)
+export(plotNicheClusterConnectivity)
 export(plotPCA)
 export(plotPCA_2D)
 export(plotPCA_3D)