Overview | Quick start | RGraphSpace attributes | Vertex attributes | Edge attributes | Arrowhead attributes | Passing graphs to geoms | Why camelCase attribute names? | Online tutorials | Other examples | Citation | Session information | References
Package: RGraphSpace 1.5.7
Mauro Antônio Alves Castro
RGraphSpace: Rendering Graphs as Coherent Spatial Objects in 'ggplot2'
An interface for rendering 'igraph' objects as 'ggplot2' graphics within a normalized coordinate space. 'RGraphSpace' implements new geometries that treat a graph as a single coherent object, synchronizing node and edge layers under standard aesthetic mappings. Node features are resolved on demand, supporting high-dimensional data without expanding node tables. Spatial alignment is available at the pixel level, with node coordinates anchored to pixel centers through a half-pixel offset, enabling precise node positioning over external reference frames such as images and maps. Core functionality builds on 'igraph', 'ggplot2', and 'tidygraph'; optional geometry and large raster-background images use 'sf' and 'terra' when installed.
Authors:
RGraphSpace_1.5.7.tar.gz
RGraphSpace_1.5.7.zip(r-4.7-any)RGraphSpace_1.5.7.zip(r-4.6-any)RGraphSpace_1.5.7.zip(r-4.5-any)
RGraphSpace_1.5.7.tgz(r-4.6-any)RGraphSpace_1.5.7.tgz(r-4.5-any)
RGraphSpace_1.5.7.tar.gz(r-4.7-any)RGraphSpace_1.5.7.tar.gz(r-4.6-any)
RGraphSpace_1.5.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RGraphSpace/json (API)
| # Install 'RGraphSpace' in R: |
| install.packages('RGraphSpace', repos = c('https://sysbiolab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sysbiolab/rgraphspace/issues
Pkgdown/docs site:https://sysbiolab.github.io
Datasets:
- gs_image_toy - Toy 'GraphSpace' object
- gtoy1 - Toy 'igraph' objects
- gtoy2 - Toy 'igraph' objects
Last updated from:1e53a1bc40. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 191 | ||
| source / vignettes | OK | 252 | ||
| linux-release | OK | 261 | ||
| macos-release | OK | 205 | ||
| macos-oldrel | OK | 188 | ||
| windows-devel | OK | 179 | ||
| windows-release | OK | 167 | ||
| windows-oldrel | OK | 168 | ||
| wasm-release | OK | 156 |
Exports:annotation_gspace_imageas_colorrasteras.GraphSpacecropGraphSpaceedgespace_handlerfitGeometryflipGraphSpacegeom_edgespacegeom_graphspacegeom_nodespaceGeomEdgeSpaceGeomNodeSpacegetGraphSpaceglyph_legendglyph_listglyph_modeglyph_protoGlyphArrowGlyphArrowBar1GlyphArrowBar2GlyphBarGlyphBarredArrow1GlyphBarredArrow2GlyphBlock1GlyphBlock2GlyphChevron1GlyphChevron2GlyphCircle1GlyphCircle2GlyphCross1GlyphCross2GlyphDiamond1GlyphDiamond2GlyphDoubleArrow1GlyphDoubleArrow2GlyphDoubleBar1GlyphDoubleBar2GlyphHarpoon1GlyphHarpoon2GlyphNoneGlyphNotch1GlyphNotch2GlyphReverseArrow1GlyphReverseArrow2GlyphSquare1GlyphSquare2GlyphStar1GlyphStar2GlyphTriangle1GlyphTriangle2GraphSpacegs_add_edgesgs_add_edges<-gs_add_featuresgs_add_nodesgs_add_nodes<-gs_computegs_delete_e_attrgs_delete_v_attrgs_ecountgs_edge_attrgs_edge_attr<-gs_edgesgs_fdatags_fdata<-gs_featuresgs_fetch_featuresgs_geometrygs_geometry<-gs_graphgs_imagegs_image_maxpixelsgs_image_maxpixels<-gs_image<-gs_namesgs_nfeaturesgs_nodesgs_scale_factorgs_scale_factor<-gs_subset_edgesgs_subset_nodesgs_vcountgs_vertex_attrgs_vertex_attr<-inject_nodespacenodespace_handlernormalizeGeometrynormalizeGraphSpaceplotGraphSpacerotateGraphSpacesfshape_ngonsfshape_ngonssfshape_starsfshape_starsStatEdgeSpaceStatNodeSpacesummarytheme_gspace_coordstheme_gspace_legendtheme_gspace_th0theme_gspace_th1theme_gspace_th2theme_gspace_th3transposeGraphSpaceupdateGraphSpace
Dependencies:base64encbeeswarmCairoclicpp11dplyrfarvergenericsggbeeswarmggplot2ggrastrgluegtableigraphisobandjsonlitelabelinglatticelifecyclemagrittrMatrixpillarpkgconfigpngpurrrR6raggRColorBrewerrlangS7scalesstringistringrsystemfontstextshapingtibbletidygraphtidyrtidyselectutf8vctrsviporviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Annotate a GraphSpace Plot with an Image | annotation_gspace_image |
| Map numeric values to a color raster | as_colorraster |
| Convert objects to GraphSpace | as.GraphSpace as.GraphSpace.data.frame as.GraphSpace.default as.GraphSpace.DFrame as.GraphSpace.igraph as.GraphSpace.matrix as.GraphSpace.Seurat as.GraphSpace.SpatialExperiment as.GraphSpace.tbl_graph |
| Crop, rotate, flip, and transpose a GraphSpace | cropGraphSpace cropGraphSpace,GraphSpace-method flipGraphSpace flipGraphSpace,GraphSpace-method rotateGraphSpace rotateGraphSpace,GraphSpace-method transposeGraphSpace transposeGraphSpace,GraphSpace-method |
| Draw edge elements in a 2D graph layout | edgespace_handler geom_edgespace |
| Convenience wrapper for node and edge geoms | geom_graphspace |
| Draw node elements in a 2D graph layout | geom_nodespace nodespace_handler |
| GeomEdgeSpace: a ggplot2 prototype for GraphSpace-class methods | GeomEdgeSpace |
| GeomNodeSpace: a ggplot2 prototype for GraphSpace-class methods | GeomNodeSpace |
| Accessors for fetching slots from a GraphSpace object | getGraphSpace getGraphSpace,GraphSpace-method |
| Using ggplot2 with GraphSpace objects | ggplot-GraphSpace ggplot.GraphSpace |
| Edge glyph prototypes | GlyphArrow GlyphArrowBar1 GlyphArrowBar2 GlyphBar GlyphBarredArrow1 GlyphBarredArrow2 GlyphBlock1 GlyphBlock2 GlyphChevron1 GlyphChevron2 GlyphCircle1 GlyphCircle2 GlyphCross1 GlyphCross2 GlyphDiamond1 GlyphDiamond2 GlyphDoubleArrow1 GlyphDoubleArrow2 GlyphDoubleBar1 GlyphDoubleBar2 GlyphHarpoon1 GlyphHarpoon2 GlyphNone GlyphNotch1 GlyphNotch2 GlyphReverseArrow1 GlyphReverseArrow2 GlyphSquare1 GlyphSquare2 GlyphStar1 GlyphStar2 GlyphTriangle1 GlyphTriangle2 glyph_collection |
| Create a standalone legend for edge glyphs | glyph_legend |
| List available edge glyphs | glyph_list plot.gs_glyph_list |
| Glyph mode of arrowType codes | glyph_mode |
| Build a new glyph prototype | glyph_proto plot.gs_glyph |
| Accessors for GraphSpace objects | $,GraphSpace-method $<-,GraphSpace-method as.igraph.GraphSpace GraphSpace-accessors gs_ecount gs_ecount,GraphSpace-method gs_edges gs_edges,GraphSpace-method gs_fdata gs_fdata,GraphSpace-method gs_fdata<- gs_fdata<-,GraphSpace-method gs_features gs_features,GraphSpace-method gs_geometry gs_geometry,GraphSpace-method gs_geometry<- gs_geometry<-,GraphSpace-method gs_graph gs_graph,GraphSpace-method gs_image gs_image,GraphSpace-method gs_image<- gs_image<-,GraphSpace-method gs_image_maxpixels gs_image_maxpixels,GraphSpace-method gs_image_maxpixels<- gs_image_maxpixels<-,GraphSpace-method gs_names gs_names,GraphSpace-method gs_nfeatures gs_nfeatures,GraphSpace-method gs_nodes gs_nodes,GraphSpace-method gs_scale_factor gs_scale_factor,GraphSpace-method gs_scale_factor<- gs_scale_factor<-,GraphSpace-method gs_vcount gs_vcount,GraphSpace-method names names,GraphSpace-method [[<-,GraphSpace-method |
| Attribute utilities for GraphSpace objects | GraphSpace-attributes gs_edge_attr gs_edge_attr,GraphSpace-method gs_edge_attr<- gs_edge_attr<-,GraphSpace-method gs_vertex_attr gs_vertex_attr,GraphSpace-method gs_vertex_attr<- gs_vertex_attr<-,GraphSpace-method |
| GraphSpace: An S4 class for igraph objects | GraphSpace-class |
| Subscript operators for GraphSpace objects | GraphSpace-subscript [,GraphSpace,ANY,ANY,ANY-method [,GraphSpace-method [[,GraphSpace,ANY,ANY-method [[,GraphSpace-method |
| Create a GraphSpace object | GraphSpace GraphSpace,ANY-method GraphSpace,data.frame-method |
| Add edges to a GraphSpace object | gs_add_edges gs_add_edges,GraphSpace-method gs_add_edges<- gs_add_edges<-,GraphSpace-method |
| Add nodes to a GraphSpace object | gs_add_nodes gs_add_nodes,GraphSpace-method gs_add_nodes<- gs_add_nodes<-,GraphSpace-method |
| Apply igraph functions to the graph inside a GraphSpace | gs_compute |
| Manipulate node features in a GraphSpace object | gs_add_features gs_features-utils gs_fetch_features |
| Toy 'GraphSpace' object | gs_image_toy |
| Filter nodes and edges in a GraphSpace object | gs_subset gs_subset_edges gs_subset_nodes |
| Toy 'igraph' objects | gtoy1 gtoy2 gtoys |
| Dynamic Scale Injection for Edge Clipping | inject_nodespace |
| Normalize or fit node geometry | fitGeometry fitGeometry,GraphSpace-method normalizeGeometry normalizeGeometry,GraphSpace-method |
| Normalize node coordinates to graph and image spaces | normalizeGraphSpace normalizeGraphSpace,GraphSpace-method |
| Plot GraphSpace objects | plot.GraphSpace |
| Wrapper function to plot GraphSpace objects in ggplot2 | plotGraphSpace plotGraphSpace,GraphSpace-method plotGraphSpace,gs_graph-method plotGraphSpace,igraph-method plotGraphSpace,tbl_graph-method |
| Build regular polygons | sfshape_ngon sfshape_ngons |
| Build star polygons | sfshape_star sfshape_stars |
| Attribute Processing for GeomEdgeSpace | StatEdgeSpace |
| Attribute Processing for GeomNodeSpace | StatNodeSpace |
| Summarise a GraphSpace object | summary,GraphSpace-method |
| RGraphSpace ggplot2 themes | theme_gspace theme_gspace_coords theme_gspace_legend theme_gspace_th0 theme_gspace_th1 theme_gspace_th2 theme_gspace_th3 |
| Update a GraphSpace object | updateGraphSpace updateGraphSpace,GraphSpace-method |