plot_congenital_annotations: Plot congenital annotations

In neurogenomics/MultiEWCE: Multi-Scale Target Explorer

Plot congenital annotations

Description

Test whether there is a difference in proportion if significantly associated fetal and non-fetal cell types across phenotypes with congenital onset vs. those without.

Usage

plot_congenital_annotations(
  results,
  gpt_annot = HPOExplorer::gpt_annot_codify(),
  hpo = HPOExplorer::get_hpo(),
  fetal_keywords = c("fetal", "fetus", "primordial", "hESC", "embryonic"),
  celltype_col = "author_celltype",
  x_var = c("fetal_celltype", "fetal_only"),
  remove_annotations = c("varies"),
  keep_descendants = NULL,
  by_branch = FALSE,
  q_threshold = 0.05,
  package = "palettetown",
  palette = "mewtwo",
  proportion.test = TRUE,
  add_baseline = TRUE,
  save_path = NULL,
  ...
)

Arguments

results	The cell type-phenotype enrichment results generated by gen_results and merged together with merge_results
gpt_annot	A data.table of GPT annotations.
hpo	Human Phenotype Ontology object, loaded from get_ontology.
fetal_keywords	A character vector of keywords to identify fetal cell types.
celltype_col	The column name of the cell type.
x_var	X-axis variable to plot.
remove_annotations	A character vector of annotations to remove.
keep_descendants	Terms whose descendants should be kept (including themselves). Set to NULL (default) to skip this filtering step.
by_branch	Use HPO ancestors as the x-axis instead of the frequency of congenital onset.
q_threshold	The q value threshold to subset the results by.
package, palette	Name of the package from which the given palette is to be extracted. The available palettes and packages can be checked by running View(paletteer::palettes_d_names).
proportion.test	Decides whether proportion test for x variable is to be carried out for each level of y. Defaults to results.subtitle. In ggbarstats, only p-values from this test will be displayed.
add_baseline	Add a horizontal line showing the proportions expected by random.
save_path	The path to save the plot.
...	Arguments passed on to ggstatsplot::ggbarstats data A data frame (or a tibble) from which variables specified are to be taken. Other data types (e.g., matrix,table, array, etc.) will not be accepted. Additionally, grouped data frames from {dplyr} should be ungrouped before they are entered as data. x The variable to use as the rows in the contingency table. Please note that if there are empty factor levels in your variable, they will be dropped. y The variable to use as the columns in the contingency table. Please note that if there are empty factor levels in your variable, they will be dropped. Default is NULL. If NULL, one-sample proportion test (a goodness of fit test) will be run for the x variable. Otherwise an appropriate association test will be run. This argument can not be NULL for ggbarstats function. counts The variable in data containing counts, or NULL if each row represents a single observation. type A character specifying the type of statistical approach: "parametric" "nonparametric" "robust" "bayes" You can specify just the initial letter. paired Logical indicating whether data came from a within-subjects or repeated measures design study (Default: FALSE). results.subtitle Decides whether the results of statistical tests are to be displayed as a subtitle (Default: TRUE). If set to FALSE, only the plot will be returned. label Character decides what information needs to be displayed on the label in each pie slice. Possible options are "percentage" (default), "counts", "both". label.args Additional aesthetic arguments that will be passed to ggplot2::geom_label(). sample.size.label.args Additional aesthetic arguments that will be passed to ggplot2::geom_text(). digits Number of digits for rounding or significant figures. May also be "signif" to return significant figures or "scientific" to return scientific notation. Control the number of digits by adding the value as suffix, e.g. digits = "scientific4" to have scientific notation with 4 decimal places, or digits = "signif5" for 5 significant figures (see also signif()). digits.perc Numeric that decides number of decimal places for percentage labels (Default: 0L). bf.message Logical that decides whether to display Bayes Factor in favor of the null hypothesis. This argument is relevant only for parametric test (Default: TRUE). ratio A vector of proportions: the expected proportions for the proportion test (should sum to 1). Default is NULL, which means the null is equal theoretical proportions across the levels of the nominal variable. E.g., ratio = c(0.5, 0.5) for two levels, ratio = c(0.25, 0.25, 0.25, 0.25) for four levels, etc. conf.level Scalar between 0 and 1 (default: ⁠95%⁠ confidence/credible intervals, 0.95). If NULL, no confidence intervals will be computed. sampling.plan Character describing the sampling plan. Possible options are "indepMulti" (independent multinomial; default), "poisson", "jointMulti" (joint multinomial), "hypergeom" (hypergeometric). For more, see ?BayesFactor::contingencyTableBF(). fixed.margin For the independent multinomial sampling plan, which margin is fixed ("rows" or "cols"). Defaults to "rows". prior.concentration Specifies the prior concentration parameter, set to 1 by default. It indexes the expected deviation from the null hypothesis under the alternative, and corresponds to Gunel and Dickey's (1974) "a" parameter. title The text for the plot title. subtitle The text for the plot subtitle. Will work only if results.subtitle = FALSE. caption The text for the plot caption. This argument is relevant only if bf.message = FALSE. legend.title Title text for the legend. xlab Label for x axis variable. If NULL (default), variable name for x will be used. ylab Labels for y axis variable. If NULL (default), variable name for y will be used. ggtheme A {ggplot2} theme. Default value is ggstatsplot::theme_ggstatsplot(). Any of the {ggplot2} themes (e.g., theme_bw()), or themes from extension packages are allowed (e.g., ggthemes::theme_fivethirtyeight(), hrbrthemes::theme_ipsum_ps(), etc.). But note that sometimes these themes will remove some of the details that {ggstatsplot} plots typically contains. For example, if relevant, ggbetweenstats() shows details about multiple comparison test as a label on the secondary Y-axis. Some themes (e.g. ggthemes::theme_fivethirtyeight()) will remove the secondary Y-axis and thus the details as well. package,palette Name of the package from which the given palette is to be extracted. The available palettes and packages can be checked by running View(paletteer::palettes_d_names). ggplot.component A ggplot component to be added to the plot prepared by {ggstatsplot}. This argument is primarily helpful for grouped_ variants of all primary functions. Default is NULL. The argument should be entered as a {ggplot2} function or a list of {ggplot2} functions.

Examples

results <- load_example_results()
results2 <- plot_congenital_annotations(results=results)

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