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All functions

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