prioritise_targets_grid: Prioritise targets grid

In neurogenomics/MultiEWCE: Multi-Scale Target Explorer

Prioritise targets grid

Description

Plot the output of prioritise_targets as a grid.

Usage

prioritise_targets_grid(
  top_targets,
  res_class = HPOExplorer::gpt_annot_class(),
  n_per_class = 10,
  keep_severity_class = c("profound", "severe"),
  keep_physical_malformations = NULL,
  species_list = c("Homo sapiens", "Macaca mulatta", "Mus musculus", "Danio rerio",
    "Drosophila melanogaster", "Caenorhabditis elegans"),
  legend.position = "left",
  keep_ont_levels = NULL,
  width = 70,
  widths1 = c(1, 4),
  widths2 = c(1, 0.8),
  show_plot = TRUE,
  ...
)

Arguments

top_targets	output of prioritise_targets.
res_class	Output of the gpt_annot_class function.
n_per_class	Number of phenotypes per severity class to include.
keep_severity_class	Phenotypes to keep based on severity classes.
keep_physical_malformations	Phenotypes to keep based on physical malformation frequency (0=never, 1=rarely, 2=often, 3=always).
species_list	Species to include in orthologous genes grid.
legend.position	the default position of legends ("none", "left", "right", "bottom", "top", "inside")
keep_ont_levels	Only keep phenotypes at certain absolute ontology levels to keep. See add_ont_lvl for details.
width	Width of the saved plot.
widths1	Proportional widths of severity annotation heatmap (left subplot) and the top targets/orthologous genes grid (right subplot).
widths2	Proportional widths of the top targets/orthologous genes grid.
show_plot	Print the plot to the console.
...	Arguments passed on to HPOExplorer::plot_top_phenos keep_descendants Terms whose descendants should be kept (including themselves). Set to NULL (default) to skip this filtering step. annotation_order The order of the annotations to include. split_by_congenital Split the phenotypes by congenital onset (congenital = always/often, noncongenital = never/rarely). axis.text.x Whether to include x-axis text in top and bottom subplots.

Value

A named list with data and patchwork object.

Examples

top_targets <- MSTExplorer::example_targets$top_targets
out <- prioritise_targets_grid(top_targets = top_targets)

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