MAGMA tile plot

Used after merging results from multiple GWAS studies.

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()
#> see ?ewceData and browseVignettes('ewceData') for documentation
#> loading from cache
tile_res <- magma_tileplot(ctd=ctd, results=results)
#> Saving plot ==> /tmp/RtmpUbtMhH/MAGMA_Figures/Tileplots/CombinedRes_TilePlot_MAGMA_wtDendro_level1_.pdf
#> Warning: Using size for a discrete variable is not advised.
#> Warning: Using size for a discrete variable is not advised.