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stemangiolastemangiola
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solve BioCheck
1 parent 672cf44 commit 0b9ad80

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lines changed

‎NAMESPACE

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@@ -21,7 +21,6 @@ export(get_output_samples)
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export(plot_1D_intervals)
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export(plot_2D_intervals)
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export(sccomp_boxplot)
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export(sccomp_calculate_residuals)
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export(sccomp_estimate)
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export(sccomp_predict)
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export(sccomp_proportional_fold_change)

‎R/methods.R

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@@ -73,7 +73,9 @@
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#'
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#' @examples
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#'
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#' message("Use the following example after having installed cmdstanr with install.packages(\"cmdstanr\", repos = c(\"https://stan-dev.r-universe.dev/\", getOption(\"repos\")))")
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#' print("cmdstanr is needed to run this example.")
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#' # Note: Before running the example, ensure that the 'cmdstanr' package is installed:
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#' # install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev/", getOption("repos")))
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#'
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#' \donttest{
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#' if (instantiate::stan_cmdstan_exists()) {
@@ -601,7 +603,9 @@ sccomp_estimate.data.frame <- function(.data,
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#'
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#' @examples
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#'
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#' message("Use the following example after having installed install.packages(\"cmdstanr\", repos = c(\"https://stan-dev.r-universe.dev/\", getOption(\"repos\")))")
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#' print("cmdstanr is needed to run this example.")
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#' # Note: Before running the example, ensure that the 'cmdstanr' package is installed:
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#' # install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev/", getOption("repos")))
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#'
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#' \donttest{
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#' if (instantiate::stan_cmdstan_exists()) {
@@ -1036,7 +1040,9 @@ sccomp_remove_outliers.sccomp_tbl = function(.estimate,
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#'
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#' @examples
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#'
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#' message("Use the following example after having installed install.packages(\"cmdstanr\", repos = c(\"https://stan-dev.r-universe.dev/\", getOption(\"repos\")))")
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#' print("cmdstanr is needed to run this example.")
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#' # Note: Before running the example, ensure that the 'cmdstanr' package is installed:
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#' # install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev/", getOption("repos")))
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#'
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#' \donttest{
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#' if (instantiate::stan_cmdstan_exists()) {
@@ -1223,7 +1229,9 @@ sccomp_test.sccomp_tbl = function(.data,
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#'
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#' @examples
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#'
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#' message("Use the following example after having installed install.packages(\"cmdstanr\", repos = c(\"https://stan-dev.r-universe.dev/\", getOption(\"repos\")))")
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#' print("cmdstanr is needed to run this example.")
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#' # Note: Before running the example, ensure that the 'cmdstanr' package is installed:
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#' # install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev/", getOption("repos")))
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#'
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#' \donttest{
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#' if (instantiate::stan_cmdstan_exists() && .Platform$OS.type == "unix") {
@@ -1325,7 +1333,9 @@ sccomp_replicate.sccomp_tbl = function(fit,
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#'
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#' @examples
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#'
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#' message("Use the following example after having installed install.packages(\"cmdstanr\", repos = c(\"https://stan-dev.r-universe.dev/\", getOption(\"repos\")))")
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#' print("cmdstanr is needed to run this example.")
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#' # Note: Before running the example, ensure that the 'cmdstanr' package is installed:
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#' # install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev/", getOption("repos")))
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#'
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#' \donttest{
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#' if (instantiate::stan_cmdstan_exists() && .Platform$OS.type == "unix") {
@@ -1468,6 +1478,11 @@ sccomp_predict.sccomp_tbl = function(fit,
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#'
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#' @export
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#'
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#' print("cmdstanr is needed to run this example.")
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#' # Note: Before running the example, ensure that the 'cmdstanr' package is installed:
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#' # install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev/", getOption("repos")))
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#'
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#'
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#' @examples
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#' \donttest{
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#' if (instantiate::stan_cmdstan_exists() && .Platform$OS.type == "unix") {
@@ -1568,7 +1583,9 @@ sccomp_calculate_residuals.sccomp_tbl = function(.data){
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#'
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#' @examples
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#'
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#' message("Use the following example after having installed cmdstanr with install.packages(\"cmdstanr\", repos = c(\"https://stan-dev.r-universe.dev/\", getOption(\"repos\")))")
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#' print("cmdstanr is needed to run this example.")
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#' # Note: Before running the example, ensure that the 'cmdstanr' package is installed:
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#' # install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev/", getOption("repos")))
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#'
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#' \donttest{
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#' if (instantiate::stan_cmdstan_exists()) {
@@ -1702,7 +1719,9 @@ sccomp_remove_unwanted_variation.sccomp_tbl = function(.data,
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#'
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#' @examples
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#'
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#' message("Use the following example after having installed install.packages(\"cmdstanr\", repos = c(\"https://stan-dev.r-universe.dev/\", getOption(\"repos\")))")
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#' print("cmdstanr is needed to run this example.")
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#' # Note: Before running the example, ensure that the 'cmdstanr' package is installed:
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#' # install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev/", getOption("repos")))
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#'
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#' \donttest{
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#' if (instantiate::stan_cmdstan_exists()) {
@@ -1859,6 +1878,8 @@ simulate_data.tbl = function(.data,
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#' @export
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#'
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#' @examples
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#'
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#' print("cmdstanr is needed to run this example.")
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#' # Note: Before running the example, ensure that the 'cmdstanr' package is installed:
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#' # install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev/", getOption("repos")))
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#'
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#'
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#' @examples
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#'
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#' message("Use the following example after having installed install.packages(\"cmdstanr\", repos = c(\"https://stan-dev.r-universe.dev/\", getOption(\"repos\")))")
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#' print("cmdstanr is needed to run this example.")
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#' # Note: Before running the example, ensure that the 'cmdstanr' package is installed:
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#' # install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev/", getOption("repos")))
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#'
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#' \donttest{
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#' if (instantiate::stan_cmdstan_exists()) {
@@ -2131,6 +2154,12 @@ clear_stan_model_cache <- function(cache_dir = sccomp_stan_models_cache_dir) {
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#' }
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#'
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#' @examples
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#'
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#' print("cmdstanr is needed to run this example.")
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#' # Note: Before running the example, ensure that the 'cmdstanr' package is installed:
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#' # install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev/", getOption("repos")))
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#'
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#'
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#' \donttest{
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#' if (instantiate::stan_cmdstan_exists()) {
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#' # Load example data

‎R/utilities.R

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@@ -1843,6 +1843,8 @@ get_FDR = function(x){
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#' @return A combined plot of 1D interval plots.
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#' @examples
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#'
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#' print("cmdstanr is needed to run this example.")
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#'
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#' \donttest{
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#' if (instantiate::stan_cmdstan_exists()) {
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#' data("counts_obj")
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#' }
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#'
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#'
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plot_1D_intervals = function(.data, significance_threshold = 0.05, test_composition_above_logit_fold_change = .data |> attr("test_composition_above_logit_fold_change")){
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message("sccomp says: Some FDR-significant populations may cross the fold change threshold. \n This because, as sccomp is a Bayesian method, the FDR is calculated according to Stephens (doi: 10.1093/biostatistics/kxw041), \n by sorting the probability of the null hypothesis in ascending order and calculating the cumulative average.")
@@ -1946,9 +1947,32 @@ plot_1D_intervals = function(.data, significance_threshold = 0.05, test_composit
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#' @export
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#'
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#' @return A ggplot object representing the 2D interval plot.
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#'
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#' @examples
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#' # Example usage:
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#' # plot_2D_intervals(.data, "cell_group", theme_minimal(), 0.025)
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#'
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#' print("cmdstanr is needed to run this example.")
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#'
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#' \donttest{
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#' if (instantiate::stan_cmdstan_exists()) {
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#' data("counts_obj")
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#'
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#' estimate <- sccomp_estimate(
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#' counts_obj,
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#' ~ type,
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#' ~type,
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#' sample,
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#' cell_group,
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#' count,
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#' cores = 1
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#' ) |>
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#' sccomp_test()
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#'
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#' # Example usage:
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#' my_plot = plot_2D_intervals(estimate)
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#'
1973+
#' }
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#' }
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#'
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plot_2D_intervals = function(
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.data,
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significance_threshold = 0.05,
@@ -3925,10 +3949,6 @@ check_missing_parameters <- function(effects, model_effects) {
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}
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}
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library(dplyr)
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library(dplyr)
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harmonise_factor_levels <- function(dataframe_query, dataframe_reference) {
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# 1. Identify factor columns in the reference
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factor_cols <- names(dataframe_reference)[sapply(dataframe_reference, is.factor)]

‎man/plot.sccomp_tbl.Rd

+3-1
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‎man/plot_1D_intervals.Rd

+2
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‎man/plot_2D_intervals.Rd

+24-2
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‎man/sccomp_boxplot.Rd

+2
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‎man/sccomp_estimate.Rd

+3-1
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‎man/sccomp_predict.Rd

+3-1
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‎man/sccomp_proportional_fold_change.Rd

+6
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‎man/sccomp_remove_outliers.Rd

+3-1
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‎man/sccomp_remove_unwanted_variation.Rd

+3-1
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‎man/sccomp_replicate.Rd

+3-1
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‎man/sccomp_test.Rd

+3-1
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‎man/simulate_data.Rd

+3-1
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