Report plot

Plot the results of a filtering report generated by prioritise_targets.

report_plot(
  rep_dt,
  results,
  phenotype_to_genes = HPOExplorer::load_phenotype_to_genes(),
  annot = HPOExplorer::load_phenotype_to_genes("phenotype.hpoa"),
  remove_cols = c("Rows", "ids"),
  show_plot = TRUE,
  save_plot = tempfile(fileext = "_report_plot.pdf"),
  verbose = TRUE,
  ...
)

Arguments

rep_dt

Report table.

results

The cell type-phenotype enrichment results generated by gen_results and merged together with merge_results.

phenotype_to_genes

Output of load_phenotype_to_genes mapping phenotypes to gene annotations.

annot

HPO annotations.

remove_cols

Columns to remove from rep_dt.

show_plot

Show the plot.

save_plot

Path to save the plot to.

verbose

Print messages.

...

Arguments passed on to ggplot2::ggsave

filename

File name to create on disk.

plot

Plot to save, defaults to last plot displayed.

device

Device to use. Can either be a device function (e.g. png), or one of "eps", "ps", "tex" (pictex), "pdf", "jpeg", "tiff", "png", "bmp", "svg" or "wmf" (windows only).

path

Path of the directory to save plot to: path and filename are combined to create the fully qualified file name. Defaults to the working directory.

scale

Multiplicative scaling factor.

width,height,units

Plot size in units ("in", "cm", "mm", or "px"). If not supplied, uses the size of current graphics device.

dpi

Plot resolution. Also accepts a string input: "retina" (320), "print" (300), or "screen" (72). Applies only to raster output types.

limitsize

When TRUE (the default), ggsave() will not save images larger than 50x50 inches, to prevent the common error of specifying dimensions in pixels.

bg

Background colour. If NULL, uses the plot.background fill value from the plot theme.

Value

ggplot object

Examples

results <- load_example_results()
rep_dt <- example_targets$report
gp <- report_plot(rep_dt=rep_dt, results=results)
#> report_plot:: Preparing data.
#> Reading cached RDS file: phenotype.hpoa
#> + Version: v2023-10-09
#> Reading cached RDS file: phenotype_to_genes.txt
#> + Version: v2023-10-09
#> Loading required namespace: rvest
#> report_plot:: Preparing plot.
#> Warning: The `facets` argument of `facet_grid()` is deprecated as of ggplot2 2.2.0.
#> ℹ Please use the `rows` argument instead.
#> ℹ The deprecated feature was likely used in the MultiEWCE package.
#>   Please report the issue at
#>   <https://github.com/neurogenomics/MultiEWCE/issues>.
#> Saving plot ==> /tmp/Rtmp0tNWxK/file26a92ff8c571_report_plot.pdf
#> Saving 6.67 x 6.67 in image