Package: SCpubr 3.0.1

SCpubr: Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

A system that provides a streamlined way of generating publication ready plots for known Single-Cell transcriptomics data in a “publication ready” format. This is, the goal is to automatically generate plots with the highest quality possible, that can be used right away or with minimal modifications for a research article.

Authors:Enrique Blanco-Carmona [cre, aut]

SCpubr_3.0.1.tar.gz
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SCpubr_3.0.1.tgz(r-4.6-any)SCpubr_3.0.1.tgz(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SCpubr/json (API)

# Install 'SCpubr' in R:

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

Bug tracker:https://github.com/enblacar/scpubr/issues

Datasets:

human_chr_locations - Chromosome arm locations for human genome GRCh38.

On CRAN:

software singlecell visualization data-visualization ggplot2 publication-quality-plots seurat single-cell single-cell-genomics single-cell-rna-seq

9.44 score 223 stars 1 packages 413 scripts 1.1k downloads 34 exports 0 dependencies

Last updated from:a3ae2999ce. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	318
source / vignettes	OK	382
linux-release-x86_64	OK	300
macos-release-arm64	OK	305
macos-oldrel-arm64	OK	286
windows-devel	OK	455
windows-release	OK	531
windows-oldrel	OK	460
wasm-release	OK	223

Exports:do_ActivityHeatmap do_AlluvialPlot do_BarPlot do_BeeSwarmPlot do_BoxPlot do_CellularStatesPlot do_ChordDiagramPlot do_CNVHeatmap do_ColorBlindCheck do_ColorPalette do_CorrelationHeatmap do_DimPlot do_DotPlot do_EnrichmentHeatmap do_ExpressionHeatmap do_FeaturePlot do_GroupwiseDEHeatmap do_LigandReceptorPlot do_LoadingsHeatmap do_MetadataHeatmap do_NebulosaPlot do_PackageReport do_PathwayActivityHeatmap do_RankedEnrichmentHeatmap do_RankedExpressionHeatmap do_RidgePlot do_SCEnrichmentHeatmap do_SCExpressionHeatmap do_StripPlot do_TermEnrichmentPlot do_TFActivityHeatmap do_ViolinPlot do_VolcanoPlot do_WafflePlot

Dependencies:

reference_manual

Rendered fromreference_manual.Rmdusingknitr::rmarkdown

Last update: 2023-07-31
Started: 2022-10-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Compute affinity of gene sets to cell populations using decoupleR.	do_ActivityHeatmap
Generate Alluvial plots.	do_AlluvialPlot
Create Bar Plots.	do_BarPlot
Generate BeeSwarm plots of ranked cells colored by gene expression or metadata.	do_BeeSwarmPlot
Generate Box Plots.	do_BoxPlot
Plot relationships between enrichment scores to infer cellular states.	do_CellularStatesPlot
Generate a Chord diagram.	do_ChordDiagramPlot
Display CNV scores from inferCNV as Feature Plots.	do_CNVHeatmap
Generate colorblind variations of a given color palette.	do_ColorBlindCheck
Generate color scales based on a value.	do_ColorPalette
Create correlation matrix heatmaps.	do_CorrelationHeatmap
Generate dimensional reduction plots from a Seurat object.	do_DimPlot
Generate Dot plots of gene expression across cell groups.	do_DotPlot
Create enrichment scores heatmaps.	do_EnrichmentHeatmap
Create heatmaps of averaged expression by groups.	do_ExpressionHeatmap
Plot gene expression on dimensional reduction embeddings.	do_FeaturePlot
Compute a dotplot with the results of a group-wise DE analysis.	do_GroupwiseDEHeatmap
Visualize Ligand-Receptor analysis output.	do_LigandReceptorPlot
Compute a heatmap summary of the top and bottom genes in the PCA loadings for the desired PCs in a Seurat object.	do_LoadingsHeatmap
Compute a heatmap of categorical variables.	do_MetadataHeatmap
Plot kernel density estimates of gene expression on dimensional reduction embeddings.	do_NebulosaPlot
Generate a status report of SCpubr and its dependencies.	do_PackageReport
Plot Pathway Activities from decoupleR using Progeny prior knowledge.	do_PathwayActivityHeatmap
Compute a heatmap of enrichment of gene sets on the context of a dimensional reduction component.	do_RankedEnrichmentHeatmap
Compute a heatmap of expression of genes on the context of a dimensional reduction component.	do_RankedExpressionHeatmap
Create ridge plots.	do_RidgePlot
Perform a single-cell-based heatmap showing the enrichment in a list of gene sets.	do_SCEnrichmentHeatmap
Perform a single-cell-based heatmap showing the expression of genes.	do_SCExpressionHeatmap
Generate a Strip plot.	do_StripPlot
Display the enriched terms for a given list of genes.	do_TermEnrichmentPlot
Plot TF Activities from decoupleR using Dorothea prior knowledge.	do_TFActivityHeatmap
Generate Violin plots from a Seurat object.	do_ViolinPlot
Compute a Volcano plot out of DE genes.	do_VolcanoPlot
Generate Waffle plots to display cell group proportions.	do_WafflePlot
Chromosome arm locations for human genome GRCh38.	human_chr_locations