From 04d0e6bab26e84467be662a12d750d7b03645b60 Mon Sep 17 00:00:00 2001 From: jiajic <72078254+jiajic@users.noreply.github.com> Date: Wed, 1 May 2024 15:12:35 -0400 Subject: [PATCH] Chore: update for GiottoClass & GiottoVisuals --- DESCRIPTION | 5 +++-- NAMESPACE | 7 +++++++ R/suite_reexports.R | 12 +++++++++--- man/crossSectionGenePlot.Rd | 2 +- man/reexports.Rd | 5 ++++- 5 files changed, 24 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index ad62d7b3b..0c7ca306c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -32,7 +32,7 @@ Depends: utils (>= 3.5.0), R (>= 3.5.0), methods, - GiottoClass (>= 0.2.4) + GiottoClass (>= 0.3.0) Imports: BiocParallel, BiocSingular, @@ -43,7 +43,7 @@ Imports: ggplot2 (>= 3.1.1), ggrepel, GiottoUtils (>= 0.1.6), - GiottoVisuals (>= 0.1.1), + GiottoVisuals (>= 0.2.0), igraph (>= 1.2.4.1), jsonlite, limma, @@ -148,6 +148,7 @@ Collate: 'suite_reexports.R' 'image_registration.R' 'interactivity.R' + 'kriging.R' 'package_imports.R' 'poly_influence.R' 'python_hmrf.R' diff --git a/NAMESPACE b/NAMESPACE index 8ed41889e..55032e2cd 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -156,6 +156,7 @@ export(detectSpatialPatterns) export(dimCellPlot) export(dimCellPlot2D) export(dimFeatPlot2D) +export(dimFeatPlot3D) export(dimGenePlot3D) export(dimPlot) export(dimPlot2D) @@ -429,12 +430,14 @@ export(spatDeconvPlot) export(spatDimCellPlot) export(spatDimCellPlot2D) export(spatDimFeatPlot2D) +export(spatDimFeatPlot3D) export(spatDimGenePlot3D) export(spatDimPlot) export(spatDimPlot2D) export(spatDimPlot3D) export(spatFeatPlot2D) export(spatFeatPlot2D_single) +export(spatFeatPlot3D) export(spatGenePlot3D) export(spatIDs) export(spatInSituPlotDensity) @@ -484,6 +487,7 @@ export(violinPlot) export(wrap) export(writeGiottoLargeImage) export(writeHMRFresults) +exportMethods(interpolateFeature) import(GiottoClass) import(GiottoUtils) import(GiottoVisuals) @@ -716,6 +720,7 @@ importFrom(GiottoVisuals,addGiottoImageToSpatPlot) importFrom(GiottoVisuals,dimCellPlot) importFrom(GiottoVisuals,dimCellPlot2D) importFrom(GiottoVisuals,dimFeatPlot2D) +importFrom(GiottoVisuals,dimFeatPlot3D) importFrom(GiottoVisuals,dimGenePlot3D) importFrom(GiottoVisuals,dimPlot) importFrom(GiottoVisuals,dimPlot2D) @@ -750,12 +755,14 @@ importFrom(GiottoVisuals,spatDeconvPlot) importFrom(GiottoVisuals,spatDimCellPlot) importFrom(GiottoVisuals,spatDimCellPlot2D) importFrom(GiottoVisuals,spatDimFeatPlot2D) +importFrom(GiottoVisuals,spatDimFeatPlot3D) importFrom(GiottoVisuals,spatDimGenePlot3D) importFrom(GiottoVisuals,spatDimPlot) importFrom(GiottoVisuals,spatDimPlot2D) importFrom(GiottoVisuals,spatDimPlot3D) importFrom(GiottoVisuals,spatFeatPlot2D) importFrom(GiottoVisuals,spatFeatPlot2D_single) +importFrom(GiottoVisuals,spatFeatPlot3D) importFrom(GiottoVisuals,spatGenePlot3D) importFrom(GiottoVisuals,spatInSituPlotDensity) importFrom(GiottoVisuals,spatInSituPlotHex) diff --git a/R/suite_reexports.R b/R/suite_reexports.R index d84a72632..b6529e3eb 100644 --- a/R/suite_reexports.R +++ b/R/suite_reexports.R @@ -473,7 +473,9 @@ GiottoVisuals::dimCellPlot2D #' @export GiottoVisuals::dimFeatPlot2D #' @export -GiottoVisuals::dimGenePlot3D +GiottoVisuals::dimGenePlot3D # TODO remove in next version +#' @export +GiottoVisuals::dimFeatPlot3D #' @export GiottoVisuals::dimPlot #' @export @@ -545,7 +547,9 @@ GiottoVisuals::spatDimCellPlot2D #' @export GiottoVisuals::spatDimFeatPlot2D #' @export -GiottoVisuals::spatDimGenePlot3D +GiottoVisuals::spatDimGenePlot3D # TODO remove in next version +#' @export +GiottoVisuals::spatDimFeatPlot3D #' @export GiottoVisuals::spatDimPlot #' @export @@ -557,7 +561,9 @@ GiottoVisuals::spatFeatPlot2D #' @export GiottoVisuals::spatFeatPlot2D_single #' @export -GiottoVisuals::spatGenePlot3D +GiottoVisuals::spatGenePlot3D # TODO remove in next version +#' @export +GiottoVisuals::spatFeatPlot3D #' @export GiottoVisuals::spatPlot #' @export diff --git a/man/crossSectionGenePlot.Rd b/man/crossSectionGenePlot.Rd index 084a99be8..6dc072505 100644 --- a/man/crossSectionGenePlot.Rd +++ b/man/crossSectionGenePlot.Rd @@ -39,5 +39,5 @@ Visualize cells and gene expression in a virtual cross section according to spat Description of parameters. } \seealso{ -\link[GiottoVisuals:spatGenePlot3D]{GiottoVisuals::spatGenePlot3D} and \link[GiottoVisuals:spatFeatPlot2D]{GiottoVisuals::spatFeatPlot2D} +\link[GiottoVisuals:spatFeatPlot3D]{GiottoVisuals::spatGenePlot3D} and \link[GiottoVisuals:spatFeatPlot2D]{GiottoVisuals::spatFeatPlot2D} } diff --git a/man/reexports.Rd b/man/reexports.Rd index 2cc74eacd..6f6d4ab15 100644 --- a/man/reexports.Rd +++ b/man/reexports.Rd @@ -226,6 +226,7 @@ \alias{dimCellPlot2D} \alias{dimFeatPlot2D} \alias{dimGenePlot3D} +\alias{dimFeatPlot3D} \alias{dimPlot} \alias{dimPlot2D} \alias{dimPlot3D} @@ -262,12 +263,14 @@ \alias{spatDimCellPlot2D} \alias{spatDimFeatPlot2D} \alias{spatDimGenePlot3D} +\alias{spatDimFeatPlot3D} \alias{spatDimPlot} \alias{spatDimPlot2D} \alias{spatDimPlot3D} \alias{spatFeatPlot2D} \alias{spatFeatPlot2D_single} \alias{spatGenePlot3D} +\alias{spatFeatPlot3D} \alias{spatPlot} \alias{spatPlot2D} \alias{spatPlot3D} @@ -290,6 +293,6 @@ below to see their documentation. \item{GiottoUtils}{\code{\link[GiottoUtils:pipe]{\%>\%}}, \code{\link[GiottoUtils]{getDistinctColors}}, \code{\link[GiottoUtils]{getRainbowColors}}} - \item{GiottoVisuals}{\code{\link[GiottoVisuals]{addGiottoImageToSpatPlot}}, \code{\link[GiottoVisuals]{dimCellPlot}}, \code{\link[GiottoVisuals:dimCellPlot]{dimCellPlot2D}}, \code{\link[GiottoVisuals]{dimFeatPlot2D}}, \code{\link[GiottoVisuals]{dimGenePlot3D}}, \code{\link[GiottoVisuals]{dimPlot}}, \code{\link[GiottoVisuals:dimPlot]{dimPlot2D}}, \code{\link[GiottoVisuals:dimPlot]{dimPlot3D}}, \code{\link[GiottoVisuals]{getColors}}, \code{\link[GiottoVisuals]{giottoSankeyPlan}}, \code{\link[GiottoVisuals]{plotHeatmap}}, \code{\link[GiottoVisuals]{plotMetaDataCellsHeatmap}}, \code{\link[GiottoVisuals]{plotMetaDataHeatmap}}, \code{\link[GiottoVisuals]{plotPCA}}, \code{\link[GiottoVisuals]{plotPCA_2D}}, \code{\link[GiottoVisuals]{plotPCA_3D}}, \code{\link[GiottoVisuals]{plotStatDelaunayNetwork}}, \code{\link[GiottoVisuals]{plotTSNE}}, \code{\link[GiottoVisuals]{plotTSNE_2D}}, \code{\link[GiottoVisuals]{plotTSNE_3D}}, \code{\link[GiottoVisuals]{plotUMAP}}, \code{\link[GiottoVisuals]{plotUMAP_2D}}, \code{\link[GiottoVisuals]{plotUMAP_3D}}, \code{\link[GiottoVisuals]{sankeyLabel}}, \code{\link[GiottoVisuals:sankeyLabel]{sankeyLabel<-}}, \code{\link[GiottoVisuals]{sankeyPlot}}, \code{\link[GiottoVisuals]{sankeyRelate}}, \code{\link[GiottoVisuals:sankeyRelate]{sankeyRelate<-}}, \code{\link[GiottoVisuals]{sankeySet}}, \code{\link[GiottoVisuals]{sankeySetAddresses}}, \code{\link[GiottoVisuals]{showClusterDendrogram}}, \code{\link[GiottoVisuals]{showClusterHeatmap}}, \code{\link[GiottoVisuals]{showColorInstructions}}, \code{\link[GiottoVisuals]{showSaveParameters}}, \code{\link[GiottoVisuals]{spatCellPlot}}, \code{\link[GiottoVisuals:spatCellPlot]{spatCellPlot2D}}, \code{\link[GiottoVisuals]{spatDeconvPlot}}, \code{\link[GiottoVisuals]{spatDimCellPlot}}, \code{\link[GiottoVisuals]{spatDimCellPlot2D}}, \code{\link[GiottoVisuals]{spatDimFeatPlot2D}}, \code{\link[GiottoVisuals]{spatDimGenePlot3D}}, \code{\link[GiottoVisuals]{spatDimPlot}}, \code{\link[GiottoVisuals:spatDimPlot]{spatDimPlot2D}}, \code{\link[GiottoVisuals]{spatDimPlot3D}}, \code{\link[GiottoVisuals]{spatFeatPlot2D}}, \code{\link[GiottoVisuals]{spatFeatPlot2D_single}}, \code{\link[GiottoVisuals]{spatGenePlot3D}}, \code{\link[GiottoVisuals]{spatInSituPlotDensity}}, \code{\link[GiottoVisuals]{spatInSituPlotHex}}, \code{\link[GiottoVisuals]{spatInSituPlotPoints}}, \code{\link[GiottoVisuals]{spatNetwDistributions}}, \code{\link[GiottoVisuals]{spatNetwDistributionsDistance}}, \code{\link[GiottoVisuals]{spatNetwDistributionsKneighbors}}, \code{\link[GiottoVisuals]{spatPlot}}, \code{\link[GiottoVisuals:spatPlot]{spatPlot2D}}, \code{\link[GiottoVisuals:spatPlot]{spatPlot3D}}, \code{\link[GiottoVisuals]{subsetSankeySet}}, \code{\link[GiottoVisuals]{violinPlot}}} + \item{GiottoVisuals}{\code{\link[GiottoVisuals]{addGiottoImageToSpatPlot}}, \code{\link[GiottoVisuals]{dimCellPlot}}, \code{\link[GiottoVisuals:dimCellPlot]{dimCellPlot2D}}, \code{\link[GiottoVisuals]{dimFeatPlot2D}}, \code{\link[GiottoVisuals]{dimFeatPlot3D}}, \code{\link[GiottoVisuals:dimFeatPlot3D]{dimGenePlot3D}}, \code{\link[GiottoVisuals]{dimPlot}}, \code{\link[GiottoVisuals:dimPlot]{dimPlot2D}}, \code{\link[GiottoVisuals:dimPlot]{dimPlot3D}}, \code{\link[GiottoVisuals]{getColors}}, \code{\link[GiottoVisuals]{giottoSankeyPlan}}, \code{\link[GiottoVisuals]{plotHeatmap}}, \code{\link[GiottoVisuals]{plotMetaDataCellsHeatmap}}, \code{\link[GiottoVisuals]{plotMetaDataHeatmap}}, \code{\link[GiottoVisuals]{plotPCA}}, \code{\link[GiottoVisuals]{plotPCA_2D}}, \code{\link[GiottoVisuals]{plotPCA_3D}}, \code{\link[GiottoVisuals]{plotStatDelaunayNetwork}}, \code{\link[GiottoVisuals]{plotTSNE}}, \code{\link[GiottoVisuals]{plotTSNE_2D}}, \code{\link[GiottoVisuals]{plotTSNE_3D}}, \code{\link[GiottoVisuals]{plotUMAP}}, \code{\link[GiottoVisuals]{plotUMAP_2D}}, \code{\link[GiottoVisuals]{plotUMAP_3D}}, \code{\link[GiottoVisuals]{sankeyLabel}}, \code{\link[GiottoVisuals:sankeyLabel]{sankeyLabel<-}}, \code{\link[GiottoVisuals]{sankeyPlot}}, \code{\link[GiottoVisuals]{sankeyRelate}}, \code{\link[GiottoVisuals:sankeyRelate]{sankeyRelate<-}}, \code{\link[GiottoVisuals]{sankeySet}}, \code{\link[GiottoVisuals]{sankeySetAddresses}}, \code{\link[GiottoVisuals]{showClusterDendrogram}}, \code{\link[GiottoVisuals]{showClusterHeatmap}}, \code{\link[GiottoVisuals]{showColorInstructions}}, \code{\link[GiottoVisuals]{showSaveParameters}}, \code{\link[GiottoVisuals]{spatCellPlot}}, \code{\link[GiottoVisuals:spatCellPlot]{spatCellPlot2D}}, \code{\link[GiottoVisuals]{spatDeconvPlot}}, \code{\link[GiottoVisuals]{spatDimCellPlot}}, \code{\link[GiottoVisuals]{spatDimCellPlot2D}}, \code{\link[GiottoVisuals]{spatDimFeatPlot2D}}, \code{\link[GiottoVisuals]{spatDimFeatPlot3D}}, \code{\link[GiottoVisuals:spatDimFeatPlot3D]{spatDimGenePlot3D}}, \code{\link[GiottoVisuals]{spatDimPlot}}, \code{\link[GiottoVisuals:spatDimPlot]{spatDimPlot2D}}, \code{\link[GiottoVisuals]{spatDimPlot3D}}, \code{\link[GiottoVisuals]{spatFeatPlot2D}}, \code{\link[GiottoVisuals]{spatFeatPlot2D_single}}, \code{\link[GiottoVisuals]{spatFeatPlot3D}}, \code{\link[GiottoVisuals:spatFeatPlot3D]{spatGenePlot3D}}, \code{\link[GiottoVisuals]{spatInSituPlotDensity}}, \code{\link[GiottoVisuals]{spatInSituPlotHex}}, \code{\link[GiottoVisuals]{spatInSituPlotPoints}}, \code{\link[GiottoVisuals]{spatNetwDistributions}}, \code{\link[GiottoVisuals]{spatNetwDistributionsDistance}}, \code{\link[GiottoVisuals]{spatNetwDistributionsKneighbors}}, \code{\link[GiottoVisuals]{spatPlot}}, \code{\link[GiottoVisuals:spatPlot]{spatPlot2D}}, \code{\link[GiottoVisuals:spatPlot]{spatPlot3D}}, \code{\link[GiottoVisuals]{subsetSankeySet}}, \code{\link[GiottoVisuals]{violinPlot}}} }}