Package index

Correlation Plotting

Functions for plotting correlation coefficients

ggcorr()

Plot scatterplot with correlation coefficients and ab-line overlaid

Axis Management

Functions for managing plot axes

axis_limits()

Manage axis limits

Text Annotations

Functions for adding text to plots

add_text_column()

Add a column of text to a ggplot

Transformations

Scale transformation utilities

get_trans()

Get transformation object

Plot Saving

Utilities for saving plots

save_plot()

Save plot in multiple formats using cowplot::save_plot

ggsave2()

Save plot in multiple formats using cowplot::ggsave2

Group Plots

Functions for visualising group characteristics

plot_group_heatmap() plot_cluster_heatmap()

Plot heat map of scaled variable values per group

plot_group_density() plot_cluster_density()

Plot density of variable values with per-group overlays

plot_group_mst() plot_cluster_mst()

Plot minimum-spanning tree of groups with per-variable node colouring

plot_group_scatter() plot_cluster_scatter()

Biaxial scatter plot with group medians overlaid

Cluster Plots (Aliases)

Aliases of group plot functions for backward compatibility

plot_group_heatmap() plot_cluster_heatmap()

Plot heat map of scaled variable values per group

plot_group_density() plot_cluster_density()

Plot density of variable values with per-group overlays

plot_group_mst() plot_cluster_mst()

Plot minimum-spanning tree of groups with per-variable node colouring

plot_group_scatter() plot_cluster_scatter()

Biaxial scatter plot with group medians overlaid

Cluster Analysis

Functions for clustering, analysing and merging clusters

cluster_louvain()

Louvain community-detection clustering

cluster_som()

Self-Organizing Map (SOM) clustering

cluster_louvain_merge()

Louvain clustering with bin and unimodal merging

cluster_som_merge()

SOM clustering with bin and unimodal merging

cluster_merge_bin()

Merge clusters based on variable bin thresholds

cluster_merge_unimodal()

Merge clusters that remain unimodal when combined

Cluster Simulation

Functions for simulating high-dimensional single-cell data

cluster_sim()

Simulate High-Dimensional Single-Cell Clusters (FAUST Method)