plot_celltype_associations: Plot celltype associations calculated using MAGMA

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

Plot celltype associations calculated using MAGMA

Description

Can take input from either calculate_celltype_associations or calculate_conditional_celltype_associations.

Usage

plot_celltype_associations(
  ctAssocs,
  ctd,
  useSignificanceLine = TRUE,
  savePDF = TRUE,
  fileTag = "",
  plotDendro = TRUE,
  gwas_title = "",
  plotLegend = TRUE,
  figsDir = NULL,
  show_plot = TRUE,
  bind_plots = FALSE,
  ncol = 1,
  verbose = TRUE
)

Arguments

ctAssocs	Output from either calculate_celltype_associations or calculate_conditional_celltype_associations.
ctd	Cell type data structure containing specificity_quantiles.
useSignificanceLine	TRUE or FALSE. Should their be a vertical line marking Bonferroni significance?
savePDF	TRUE or FALSE. Save figure to file or print to screen?
fileTag	String appended to the names of the saved PDFs, i.e. the name of the celltype data file used
plotDendro	Should the dendrogram of celltypes be shown alongside the figure? TRUE or FALSE.
gwas_title	Title to be displayed over the figure (string).
plotLegend	Should the figure legend be displayed?
figsDir	Directory where figures should be created.
show_plot	Print to the plot(s).
bind_plots	Bind the list of plots together using wrap_plots.
ncol	Number of columns to put plots into during bind_plots.
verbose	Print messages.

Value

A list of ggplot objects.

Examples

ctAssocs <- MAGMA.Celltyping::enrichment_results[[1]]$ctAssocsLinear
ctd <- ewceData::ctd()
figs <- plot_celltype_associations(ctAssocs = ctAssocs,
                                   ctd = ctd,
                                   savePDF = FALSE)

NathanSkene/MAGMA_Celltyping documentation built on Oct. 11, 2024, 7:19 a.m.