Package index • gfplot

Survival figures

plot_KMCurve(): Plot a Kaplan-Meier curve with risk table and hazard ratio
generate_time_event(): Build event indicators for one or more follow-up limits

Discrimination figures

plot_ROC(): Plot ROC curves for one or more markers
plot_TimeROC(): Plot time-dependent ROC curves
plot_MulROC(): Plot several ROC curves from separate datasets

Effect estimates

plot_forest(): Forest plot of effect estimates

Prediction performance

plot_pr_curve(): Precision-recall curve
plot_calibration(): Calibration curve
plot_decision_curve(): Decision curve

Time-to-event

plot_cumulative_incidence(): Cumulative incidence of competing events

Genomic and omics

plot_volcano(): Volcano plot
plot_waterfall(): Waterfall plot of response

Matrix and confusion

plot_heatmap(): Heatmap of a matrix
plot_confusion(): Confusion matrix

Distributions

plot_violin(): Compare distributions across groups

Projections

plot_embedding(): Grouped embedding scatter
plot_tsne(): t-SNE projection of samples coloured by group

Figure specifications

gfplot_spec(): Build a figure specification
gfplot_render(): Draw a figure from a specification
gfplot_families(): List the figures gfplot can draw

Sample-level figures

plot_RiskScore(): Plot a risk score ordered by patient
plot_Boxplot(): Boxplot with optional pairwise significance annotations
plot_barplot(): Grouped bar plot with optional significance annotations
plot_cor(): Plot the correlation between two variables

Projections and models

plot_PCA(): Principal component analysis plot
plot_UMAP(): UMAP projection plot
plot_lasso(): Plot lasso coefficient paths

Enrichment and immune figures

plot_GO(): Dot plot of enriched terms
viewGSEA(): Plot a running enrichment score for an HTSanalyzeR2 result
ggGSEA(): Plot a running enrichment score for a ranked gene list
plot_immune(): Radar chart of immune-cell infiltration by group

Helpers

get_color(): Colour palettes used by the plotting functions
gfplot_colors(): House colours by semantic role
gfplot_theme(): House theme for publication figures
gfplot_legend(): Legend layout for a set of series labels
gfplot_font_setup(): Check which devices can render the figure font
gfplot_save(): Save a figure using a device that can render the requested font