plot_top_phenos: Plot top phenotypes

In neurogenomics/HPOExplorer: Analysis and Visualisation of the Human Phenotype Ontology

Plot top phenotypes

Description

Plot the most severe phenotypes per severity class: Profound, Severe, Moderate, Mild. The exception to this is the "Mild" class, where the least severe phenotypes will be taken instead of the most severe phenotypes.

Usage

plot_top_phenos(
  res_class = gpt_annot_class(),
  keep_ont_levels = seq(3, 17),
  keep_descendants = "Phenotypic abnormality",
  n_per_class = 10,
  annotation_order = NULL,
  split_by_congenital = TRUE,
  axis.text.x = c(FALSE, TRUE),
  legend.position = "right",
  ...
)

Arguments

res_class	Output of the gpt_annot_class function.
keep_ont_levels	Only keep phenotypes at certain absolute ontology levels to keep. See add_ont_lvl for details.
keep_descendants	Terms whose descendants should be kept (including themselves). Set to NULL (default) to skip this filtering step.
n_per_class	Number of phenotypes per severity class to include.
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.
legend.position	the default position of legends ("none", "left", "right", "bottom", "top", "inside")
...	Arguments passed on to patchwork::plot_layout ncol,nrow The dimensions of the grid to create - if both are NULL it will use the same logic as facet_wrap() to set the dimensions byrow Analogous to byrow in matrix(). If FALSE the plots will be filled in in column-major order widths,heights The relative widths and heights of each column and row in the grid. Will get repeated to match the dimensions of the grid. The special value of NA/⁠-1null⁠ will behave as ⁠1null⁠ unless a fixed aspect plot is inserted in which case it will allow the dimension to expand or contract to match the aspect ratio of the content guides A string specifying how guides should be treated in the layout. 'collect' will collect guides below to the given nesting level, removing duplicates. 'keep' will stop collection at this level and let guides be placed alongside their plot. auto will allow guides to be collected if a upper level tries, but place them alongside the plot if not. If you modify default guide "position" with theme(legend.position=...) while also collecting guides you must apply that change to the overall patchwork (see example). tag_level A string ('keep' or 'new') to indicate how auto-tagging should behave. See plot_annotation(). design Specification of the location of areas in the layout. Can either be specified as a text string or by concatenating calls to area() together. See the examples for further information on use. axes A string specifying how axes should be treated. 'keep' will retain all axes in individual plots. 'collect' will remove duplicated axes when placed in the same run of rows or columns of the layout. 'collect_x' and 'collect_y' will remove duplicated x-axes in the columns or duplicated y-axes in the rows respectively. axis_titles A string specifying how axis titltes should be treated. 'keep' will retain all axis titles in individual plots. 'collect' will remove duplicated titles in one direction and merge titles in the opposite direction. 'collect_x' and 'collect_y' control this for x-axis titles and y-axis titles respectively.

Examples

res_class <- gpt_annot_class()
out <- plot_top_phenos(res_class = res_class)

neurogenomics/HPOExplorer documentation built on Aug. 24, 2024, 1:39 a.m.