Package index

Saving plots

Utilities to save plots to PNG or PDF

save_plot()

General helper to save all types of plots to file

save_plot_ls()

Save a list of plots

params_plots()

Wrapper function for standard plot parameters

Gene set enrichment plots

Utilities to save plots to PNG or PDF

get_gsea_enrichment_data()

Helper function to get the plot data for GSEA plots

plot_gse_dotplot()

Generate GSE dotplots

plot_gsea_enrichment()

Plot GSEA enrichment results

plot_blitzgsea_null()

Plot the blitzGSEA calibration

plot_blitzgsea_es_null()

Plot observed enrichment scores against the blitzGSEA null

Enrichment map plotting

Generate enrichment map plots

enrichment_map_gsea()

Generate enrichment map igraph (for GSEA)

enrichment_map_oae()

Generate enrichment map igraph (for overenrichment tests)

plot_enrichment_map_ggraph()

igraph enrichment map to ggraph plot

plot_enrichment_map_visnetwork()

igraph enrichment map to VisNetwork interactive network

Other useful plots

Other plotting helpers like for volcano plots, etc.

volcano_plot()

Create a volcano plot

params_volcano()

Wrapper function for volcano plot parameters

Single cell plotting functions

Generate different single cell plots

violin_plot_sc()

Generic violin plot function

violin_plot_sc(<CellQc>)

Per-metric violin plots from a CellQc object

violin_plot_sc(<data.table>)

Violin plot from a data.table

density_plot_sc()

Generic density plot function

density_plot_sc(<CellQc>)

Per-metric density plots from a CellQc object

density_plot_sc(<data.table>)

Density plot from a data.table

joint_plot_sc()

Generic joint plot function

joint_plot_sc(<CellQc>)

Joint QC plot from a CellQc object

joint_plot_sc(<data.table>)

Joint QC plot from a data.table

dot_plot_sc()

Dot plot of marker gene expression across groups

embedding_plot_sc()

Embedding plot coloured by an obs column

feature_plot_sc()

Feature plot over an embedding

stacked_violin_plot_sc()

Stacked violin plot of gene expression across groups

feature_scatter_plot_sc()

Scatter / hex plot of two features against each other

paga_plot_sc()

PAGA abstracted graph over an embedding

Geom extensions

Extensions around the ggplot2 universe

label_centroids()

Label Centroids in Scatter Plots

Bixverse styling options

Custom ggplot2 styling for Bixverse

theme_bx()

Bixverse ggplot2 Theme

scale_fill_bx()

Bixverse Fill Scale (Discrete)

scale_fill_bx_c()

Bixverse Fill Scale (Continuous)

scale_color_bx()

Bixverse Color Scale (Discrete)

scale_color_bx_c()

Bixverse Color Scale (Continuous)

Utility functions

General utilitys

wrap_and_truncate()

Helper function to wrap and truncate text

prepare_mitch_scores()

Generate adjusted scores for plotting mitch results