Package: ggsc 1.5.0

Guangchuang Yu

ggsc: Visualizing Single Cell and Spatial Transcriptomics

Useful functions to visualize single cell and spatial data. It supports visualizing 'Seurat', 'SingleCellExperiment' and 'SpatialExperiment' objects through grammar of graphics syntax implemented in 'ggplot2'.

Authors:Guangchuang Yu [aut, cre, cph], Shuangbin Xu [aut], Noriaki Sato [ctb]

ggsc_1.5.0.tar.gz
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ggsc.pdf |ggsc.html✨
ggsc/json (API)
NEWS

# Install 'ggsc' in R:
install.packages('ggsc', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/yulab-smu/ggsc/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On BioConductor:ggsc-1.5.0(bioc 3.21)ggsc-1.4.0(bioc 3.20)

dimensionreductiongeneexpressionsinglecellsoftwarespatialtranscriptomicsvisualization

7.61 score 43 stars 17 scripts 178 downloads 23 exports 166 dependencies

Last updated 23 days agofrom:95664cdfc2. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-win-x86_64WARNINGNov 18 2024
R-4.5-linux-x86_64WARNINGNov 18 2024
R-4.4-win-x86_64WARNINGNov 18 2024
R-4.4-mac-x86_64WARNINGNov 18 2024
R-4.4-mac-aarch64WARNINGNov 18 2024
R-4.3-win-x86_64WARNINGNov 18 2024
R-4.3-mac-x86_64WARNINGNov 18 2024
R-4.3-mac-aarch64WARNINGNov 18 2024

Exports:%<+%aesdraw_key_bgpointgeom_bgpointgeom_scattermore2plot_lisa_featuresc_dimsc_dim_countsc_dim_geom_ellipsesc_dim_geom_featuresc_dim_geom_labelsc_dim_geom_subsc_dim_subsc_dotsc_featuresc_geom_annotsc_geom_pointsc_spatialsc_violinscale_bg_color_manualscale_bg_colour_discretescale_bg_colour_manualtheme

Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsbitopsbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggfunggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppParallelRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsneS4ArraysS4VectorssassscalesscattermoresctransformSeuratSeuratObjectshinySingleCellExperimentsitmosourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsystensortibbletidydrtidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviridisLitewithrxfunxtableXVectoryamlyulab.utilszlibbioczoo

Visualizing single cell data

Guangchuang Yu and Shuangbin Xu

Rendered fromggsc.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2023-11-29
Started: 2023-09-08

Readme and manuals

Help Manual

Help pageTopics
Two-Dimensional Weighted Kernel Density Estimation And Mapping the Result To Original DimensionCalWkdeCpp
Key drawing functionsdraw_key_bgpoint
geom_bgpointgeom_bgpoint
geom_scattermore2geom_scattermore2
plot_lisa_featureplot_lisa_feature
sc_dimsc_dim sc_dim,Seurat sc_dim,Seurat-method sc_dim,SingleCellExperiment sc_dim,SingleCellExperiment-method
sc_dim_countsc_dim_count
sc_dim_geom_ellipsesc_dim_geom_ellipse
sc_dim_geom_featuresc_dim_geom_feature
sc_dim_geom_labelsc_dim_geom_label
sc_dim_geom_subsetsc_dim_geom_sub
sc_dim_subsc_dim_sub
sc_dotsc_dot sc_dot,Seurat sc_dot,Seurat-method sc_dot,SingleCellExperiment sc_dot,SingleCellExperiment-method
sc_featuresc_feature sc_feature,Seurat sc_feature,Seurat-method sc_feature,SingleCellExperiment sc_feature,SingleCellExperiment-method
add the annotation layer for ggsc objectsc_geom_annot
sc_geom_pointsc_geom_point
sc_spatialsc_spatial sc_spatial,Seurat sc_spatial,Seurat-method sc_spatial,SingleCellExperiment sc_spatial,SingleCellExperiment-method
sc_violinsc_violin sc_violin,Seurat sc_violin,Seurat-method sc_violin,SingleCellExperiment sc_violin,SingleCellExperiment-method
Create your own discrete scalescale_bg_color_identity scale_bg_color_manual scale_bg_colour_discrete scale_bg_colour_identity scale_bg_colour_manual