Package: ggsc 1.11.0

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_1.11.0.tar.gz
ggsc_1.11.0.zip(r-4.7)ggsc_1.11.0.zip(r-4.6)ggsc_1.11.0.zip(r-4.5)
ggsc_1.11.0.tgz(r-4.6-x86_64)ggsc_1.11.0.tgz(r-4.6-arm64)ggsc_1.11.0.tgz(r-4.5-x86_64)ggsc_1.11.0.tgz(r-4.5-arm64)
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ggsc_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ggsc/json (API)

# Install 'ggsc' in R:

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

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-1.11.0(bioc 3.24)ggsc-1.10.1(bioc 3.23)

dimensionreduction geneexpression singlecell software spatial transcriptomics visualization openblas cpp openmp

7.31 score 51 stars 38 scripts 23 exports 159 dependencies

Last updated from:ce7831130d. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	285
linux-devel-arm64	WARNING	418
linux-devel-x86_64	WARNING	549
source / vignettes	OK	492
linux-release-arm64	WARNING	401
linux-release-x86_64	WARNING	488
macos-release-arm64	WARNING	295
macos-release-x86_64	WARNING	625
macos-oldrel-arm64	WARNING	315
macos-oldrel-x86_64	WARNING	653
windows-devel	WARNING	532
windows-release	WARNING	570
windows-oldrel	WARNING	566
wasm-release	OK	273

Exports:%<+%aes draw_key_bgpoint geom_bgpoint geom_scattermore2 plot_lisa_feature sc_dim sc_dim_count sc_dim_geom_ellipse sc_dim_geom_feature sc_dim_geom_label sc_dim_geom_sub sc_dim_sub sc_dot sc_feature sc_geom_annot sc_geom_point sc_spatial sc_violin scale_bg_color_manual scale_bg_colour_discrete scale_bg_colour_manual theme

Dependencies:abind askpass base64enc BH Biobase BiocGenerics bitops bslib cachem caTools cli cluster codetools commonmark cowplot cpp11 crosstalk curl data.table DelayedArray deldir digest dotCall64 dplyr dqrng evaluate farver fastDummies fastmap fitdistrplus FNN fontawesome fs future future.apply generics GenomicRanges ggfun ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph IRanges irlba isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle listenv lmtest magrittr MASS Matrix MatrixGenerics matrixStats memoise mime miniUI nlme openssl otel parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppParallel RcppProgress RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra Rtsne S4Arrays S4Vectors S7 sass scales scattermore sctransform Seqinfo Seurat SeuratObject shiny SingleCellExperiment sitmo sourcetools sp spam SparseArray spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr SummarizedExperiment survival sys tensor tibble tidydr tidyr tidyselect tinytex utf8 uwot vctrs viridisLite withr xfun xtable XVector yaml yulab.utils zoo

Visualizing single cell data

Rendered fromggsc.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Two-Dimensional Weighted Kernel Density Estimation And Mapping the Result To Original Dimension	CalWkdeCpp
Key drawing functions	draw_key_bgpoint
geom_bgpoint	geom_bgpoint
geom_scattermore2	geom_scattermore2
plot_lisa_feature	plot_lisa_feature
sc_dim	sc_dim sc_dim,Seurat sc_dim,Seurat-method sc_dim,SingleCellExperiment sc_dim,SingleCellExperiment-method
sc_dim_count	sc_dim_count
sc_dim_geom_ellipse	sc_dim_geom_ellipse
sc_dim_geom_feature	sc_dim_geom_feature
sc_dim_geom_label	sc_dim_geom_label
sc_dim_geom_subset	sc_dim_geom_sub
sc_dim_sub	sc_dim_sub
sc_dot	sc_dot sc_dot,Seurat sc_dot,Seurat-method sc_dot,SingleCellExperiment sc_dot,SingleCellExperiment-method
sc_feature	sc_feature sc_feature,Seurat sc_feature,Seurat-method sc_feature,SingleCellExperiment sc_feature,SingleCellExperiment-method
add the annotation layer for ggsc object	sc_geom_annot
sc_geom_point	sc_geom_point
sc_spatial	sc_spatial sc_spatial,Seurat sc_spatial,Seurat-method sc_spatial,SingleCellExperiment sc_spatial,SingleCellExperiment-method
sc_violin	sc_violin sc_violin,Seurat sc_violin,Seurat-method sc_violin,SingleCellExperiment sc_violin,SingleCellExperiment-method
Create your own discrete scale	scale_bg_color_identity scale_bg_color_manual scale_bg_colour_discrete scale_bg_colour_identity scale_bg_colour_manual