magma_tileplot: MAGMA tile plot

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

MAGMA tile plot

Description

Used after merging results from multiple GWAS studies.

Usage

magma_tileplot(
  ctd,
  results,
  height = 13,
  width = 4,
  annotLevel = 1,
  fill = "-log10(P)",
  fileTag = "",
  output_path = tempdir(),
  qvalue_thresh = NULL,
  plotDendro = TRUE,
  show_plot = TRUE,
  bind_plots = TRUE,
  wrap_width = 50,
  verbose = TRUE
)

Arguments

ctd	Cell type data structure containing "specificity_quantiles".
results	Output from either calculate_celltype_associations or calculate_conditional_celltype_associations.
height	Height of the output tileplot.
width	Width of the output tileplot.
annotLevel	Annotation level to plot the results for.
fill	Variable in results to fill the plot tile colors by. Passed to aes_string.
fileTag	String appended to the names of the saved PDFs, i.e. the name of the celltype data file used.
output_path	Location where the results should be plotted.
qvalue_thresh	The multiple-testing corrected p-value at which to filter results (set to NULL to skip filtering).
plotDendro	Should the dendrogram of celltypes be shown alongside the figure? TRUE or FALSE.
show_plot	Print to the plot(s).
bind_plots	Bind the list of plots together using wrap_plots.
wrap_width	Width at which to wrap x-axis text labels.
verbose	Print messages.

Value

List of two ggplot objects.

Examples

res <- MAGMA.Celltyping::enrichment_results[[1]]
results <- res$ctAssocMerged$level1$results
ctd <- ewceData::ctd()
tile_res <- magma_tileplot(ctd=ctd, results=results)

NathanSkene/MAGMA_Celltyping documentation built on Aug. 21, 2023, 8:55 a.m.