Package index • GiottoVisuals

All functions

addGiottoImageToSpatPlot(): addGiottoImageToSpatPlot

combine_aes(): Combine ggplot2 aesthetics

create_cluster_dendrogram(): Create clustered expression dendrogram

dimCellPlot2D() dimCellPlot(): dimCellPlot

dimFeatPlot2D(): dimFeatPlot2D

dimFeatPlot3D() dimGenePlot3D(): dimFeatPlot3D

dimPlot2D() dimPlot() dimPlot3D(): Plot dimension reduction

dotPlot(): Create a dotplot

getColors(): getColors

get_continuous_colors(): Generate a continuous set of colors

gg_annotation_raster(<gg>,<list>) gg_annotation_raster(<gg>,<giottoImage>) gg_annotation_raster(<gg>,<giottoLargeImage>) gg_annotation_raster(<gg>,<giottoAffineImage>): Append image to ggplot as annotation_raster

gg_param(): Generate ggplot params

theme_dark2: ggplot2 plotting themes

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

all_plots_save_function() gpsparam(): Plot saving

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