Plot celltype associations calculated using MAGMA

Can take input from either calculate_celltype_associations or calculate_conditional_celltype_associations.

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()
#> see ?ewceData and browseVignettes('ewceData') for documentation
#> loading from cache
figs <- plot_celltype_associations(ctAssocs = ctAssocs,
                                   ctd = ctd,
                                   savePDF = FALSE)
#> Plotting level 1:
#> + Preparing data.
#> + Generating figure.

#> Plotting level 2:
#> + Preparing data.
#> + Generating figure.