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addGiottoImageToSpatPlot()
- addGiottoImageToSpatPlot
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create_cluster_dendrogram()
- Create clustered expression dendrogram
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dimCellPlot2D()
dimCellPlot()
- dimCellPlot
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dimFeatPlot2D()
- dimFeatPlot2D
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dimFeatPlot3D()
dimGenePlot3D()
- dimFeatPlot3D
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dimPlot2D()
dimPlot()
dimPlot3D()
- Plot dimension reduction
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getColors()
- getColors
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get_continuous_colors()
- Generate a continuous set of colors
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giottoSankeyPlan
giottoSankeyPlan-class
- S4 giottoSankeyPlan class
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`+`(<giottoSankeyPlan>,<giottoSankeyPlan>)
- hidden_aliases
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mixHSV()
- Colormixing in HSV space
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mixRGB()
- Colormixing in RGB space
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pal_names
- Color palette names
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plotHeatmap()
- plotHeatmap
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plotMetaDataCellsHeatmap()
- plotMetaDataCellsHeatmap
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plotMetaDataHeatmap()
- plotMetaDataHeatmap
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plotPCA()
- plotPCA
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plotPCA_2D()
- plotPCA_2D
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plotPCA_3D()
- plotPCA_3D
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plotStatDelaunayNetwork()
- plotStatDelaunayNetwork
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plotTSNE()
- plotTSNE
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plotTSNE_2D()
- plotTSNE_2D
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plotTSNE_3D()
- plotTSNE_3D
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plotUMAP()
- plotUMAP
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plotUMAP_2D()
- plotUMAP_2D
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plotUMAP_3D()
- plotUMAP_3D
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plotly_axis_scale_2D()
- plotly_axis_scale_2D
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plotly_axis_scale_3D()
- plotly_axis_scale_3D
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plotly_grid()
- plotly_grid
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plotly_network()
- plotly_network
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sankeyLabel()
`sankeyLabel<-`()
- Get and set the sankey labels information
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sankeyPlot(<giotto>,<giottoSankeyPlan>)
sankeyPlot(<giotto>,<character>)
sankeyPlot(<data.frame>,<missing>)
sankeyPlot(<list>,<missing>)
sankeyPlot(<giottoPolygon>,<giottoPolygon>)
- Create a sankey plot
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sankeyRelate(<giottoSankeyPlan>)
`sankeyRelate<-`(<giottoSankeyPlan>,<logical>,<data.frame>)
`sankeyRelate<-`(<giottoSankeyPlan>,<logical>,<numeric>)
`sankeyRelate<-`(<giottoSankeyPlan>,<logical>,<character>)
`sankeyRelate<-`(<giottoSankeyPlan>,<missing>,<ANY>)
`sankeyRelate<-`(<giottoSankeyPlan>,<missing>,<NULL>)
- Set a relation between two sankey sets
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sankeySet()
- Create a
giottoSankeyPlan
with one set of annotations
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sankeySetAddresses()
- Data.table of sankey set locations
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set_default_color_continuous()
set_default_color_continuous_cell()
set_default_color_continuous_poly()
set_default_color_continuous_heatmap()
set_default_color_continuous_CCcom_heatmap()
set_default_color_continuous_CCcom_dotplot()
- Set a default color for continuous values
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set_default_color_discrete()
set_default_color_discrete_cell()
set_default_color_discrete_poly()
set_default_color_discrete_feat()
set_default_color_discrete_heatmap_clus()
- Set a discrete coloring scheme
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set_default_cow_n_col()
- Set default ncols in plotting grid
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showClusterDendrogram()
- showClusterDendrogram
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showClusterHeatmap()
- showClusterHeatmap
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showColorInstructions()
- Show Giotto color instructions
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showSaveParameters()
- showSaveParameters
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simple_palette_factory()
- Generate a simple palette function
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spatCellPlot2D()
spatCellPlot()
- spatCellPlot
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spatDeconvPlot()
- spatDeconvPlot
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spatDimCellPlot()
- spatDimCellPlot
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spatDimCellPlot2D()
- spatDimCellPlot2D
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spatDimFeatPlot2D()
- spatDimFeatPlot2D
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spatDimFeatPlot3D()
spatDimGenePlot3D()
- spatDimFeatPlot3D
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spatDimPlot2D()
spatDimPlot()
- spatDimPlot
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spatDimPlot3D()
- spatDimPlot3D
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spatFeatPlot2D()
- Plot data in physical space 2D
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spatFeatPlot2D_single()
- spatFeatPlot2D_single
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spatFeatPlot3D()
spatGenePlot3D()
- spatFeatPlot3D
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spatInSituPlotDensity()
- spatInSituPlotDensity
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spatInSituPlotHex()
- spatInSituPlotHex
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spatInSituPlotPoints()
- spatInSituPlotPoints
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spatNetwDistributions()
- spatNetwDistributions
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spatNetwDistributionsDistance()
- Plot spatial distance distribution
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spatNetwDistributionsKneighbors()
- spatNetwDistributionsKneighbors
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spatPlot2D()
spatPlot()
spatPlot3D()
- spatPlot
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subsetSankeySet()
- Apply subset index on a sankey set
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violinPlot()
- violinPlot