Package: gfplot 0.6.0

Feng Gao

gfplot: Publication-Ready Figures for Cancer Bioinformatics

A compact plotting toolkit for cancer bioinformatics figures. Provides publication-ready Kaplan-Meier curves with hazard ratios, ROC and time-dependent ROC curves, multiple-ROC comparisons, risk-score distributions, PCA and UMAP projections, boxplots and correlation plots, lasso coefficient paths, enrichment plots, and immune-infiltration radar charts. Palette helpers return colour-blind-friendly colours in journal styles.

Authors:Feng Gao [aut, cre]

gfplot_0.6.0.tar.gz
gfplot_0.6.0.zip(r-4.7-any)gfplot_0.6.0.zip(r-4.6-any)gfplot_0.6.0.zip(r-4.5-any)
gfplot_0.6.0.tgz(r-4.6-any)gfplot_0.6.0.tgz(r-4.5-any)
gfplot_0.6.0.tar.gz(r-4.7-any)gfplot_0.6.0.tar.gz(r-4.6-any)
gfplot_0.6.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gfplot/json (API)

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

Bug tracker:https://github.com/gflab/gfplot/issues

Pkgdown/docs site:https://gflab.github.io

On CRAN:

Conda:

2.92 score 1 stars 167 scripts 37 exports 91 dependencies

Last updated from:d72c92e414 (on master). Checks:7 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develERROR239
source / vignettesOK229
linux-releaseERROR223
macos-releaseERROR157
macos-oldrelERROR206
windows-develERROR201
windows-releaseERROR182
windows-oldrelERROR140
wasm-releaseOK184

Exports:generate_time_eventget_colorgfplot_colorsgfplot_familiesgfplot_font_setupgfplot_legendgfplot_rendergfplot_savegfplot_specgfplot_themeggGSEAplot_barplotplot_Boxplotplot_calibrationplot_confusionplot_corplot_cumulative_incidenceplot_decision_curveplot_embeddingplot_forestplot_GOplot_heatmapplot_immuneplot_KMCurveplot_lassoplot_MulROCplot_PCAplot_pr_curveplot_RiskScoreplot_ROCplot_TimeROCplot_tsneplot_UMAPplot_violinplot_volcanoplot_waterfallviewGSEA

Dependencies:abindbackportsbootbroomcarcarDataclicolorspacecommonmarkcorrplotcowplotcpp11curlDerivdoBydplyrexactRankTestsfarverforecastFormulafracdiffgenericsggplot2ggpubrggrepelggsciggsignifggtextgluegridExtragridtextgtableisobandjpeglabelinglatticelifecyclelitedownlme4lmtestmagrittrmarkdownMASSMatrixMatrixModelsmaxstatmgcvminqamodelrmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpngpolynompROCpurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangrstatixS7scalesSparseMstringistringrsurvivalsurvminertibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrxfunxml2zoo

Readme and manuals

Help Manual

Help pageTopics
Build event indicators for one or more follow-up limitsgenerate_time_event
Colour palettes used by the plotting functionsget_color
House colours by semantic rolegfplot_colors
List the figures gfplot can drawgfplot_families
Check which devices can render the figure fontgfplot_font_setup
Legend layout for a set of series labelsgfplot_legend
Draw a figure from a specificationgfplot_render
Save a figure using a device that can render the requested fontgfplot_save
Build a figure specificationgfplot_spec
House theme for publication figuresgfplot_theme
Plot a running enrichment score for a ranked gene listggGSEA
Grouped bar plot with optional significance annotationsplot_barplot
Boxplot with optional pairwise significance annotationsplot_Boxplot
Calibration curveplot_calibration
Confusion matrixplot_confusion
Plot the correlation between two variablesplot_cor
Cumulative incidence of competing eventsplot_cumulative_incidence
Decision curveplot_decision_curve
Grouped embedding scatterplot_embedding
Forest plot of effect estimatesplot_forest
Dot plot of enriched termsplot_GO
Heatmap of a matrixplot_heatmap
Radar chart of immune-cell infiltration by groupplot_immune
Plot a Kaplan-Meier curve with risk table and hazard ratioplot_KMCurve
Plot lasso coefficient pathsplot_lasso
Plot several ROC curves from separate datasetsplot_MulROC
Principal component analysis plotplot_PCA
Precision-recall curveplot_pr_curve
Plot a risk score ordered by patientplot_RiskScore
Plot ROC curves for one or more markersplot_ROC
Plot time-dependent ROC curvesplot_TimeROC
t-SNE projection of samples coloured by groupplot_tsne
UMAP projection plotplot_UMAP
Compare distributions across groupsplot_violin
Volcano plotplot_volcano
Waterfall plot of responseplot_waterfall
Plot a running enrichment score for an HTSanalyzeR2 resultviewGSEA