plot_report: Report plot

In neurogenomics/MultiEWCE: Multi-Scale Target Explorer

Report plot

Description

Plot the results of a filtering report generated by prioritise_targets.

Usage

plot_report(
  rep_dt,
  results,
  phenotype_to_genes = HPOExplorer::load_phenotype_to_genes(1),
  annot = HPOExplorer::load_phenotype_to_genes(3),
  remove_cols = c("Rows", "Rows_diff", "ids"),
  label.size = 0.25,
  show_plot = TRUE,
  add_tiers = TRUE,
  save_path = tempfile(fileext = "_plot_report.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	Phenotype to gene mapping from load_phenotype_to_genes.
annot	HPO annotations.
remove_cols	Columns to remove from rep_dt.
label.size	Size of label border, in mm.
show_plot	Print the plot to the console.
add_tiers	Add severity tiers subplot.
save_path	Save the plot to a file. Set to NULL to not save the plot.
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). If NULL (default), the device is guessed based on the filename extension. 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 Plot size in units expressed by the units argument. If not supplied, uses the size of the current graphics device. units One of the following units in which the width and height arguments are expressed: "in", "cm", "mm" or "px". 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. create.dir Whether to create new directories if a non-existing directory is specified in the filename or path (TRUE) or return an error (FALSE, default). If FALSE and run in an interactive session, a prompt will appear asking to create a new directory when necessary.

Value

ggplot object

Examples

results <- load_example_results()
rep_dt <- example_targets$report
gp <- plot_report(rep_dt=rep_dt, results=results)

neurogenomics/MultiEWCE documentation built on Sept. 28, 2024, 2:27 a.m.