Added missing function's documentations

R/adaptive.bin.R

@@ -1,7 +1,14 @@
-#' @import tibble dplyr
-NULL
-#> NULL
-
+#' Compute densities for given masses.
+#' @description
+#' Compute the density estimation for a set of masses using kernel density estimation.
+#' It allows for intensity-weighted densities and custom bandwidth functions.
+#' @param masses A numeric vector of mass values.
+#' @param mz_tol The mass-to-charge ratio tolerance.
+#' @param intensity_weighted A logical value indicating whether to weight the densities by intensities.
+#' @param intensities A numeric vector of intensity values corresponding to the masses.
+#' @param bw_func A function to compute the bandwidth based on the masses.
+#' @param n The number of equally spaced points at which the density is to be estimated. Default is 512.
+#' @return A density object representing the estimated density of the masses.
 #' @export
 compute_densities <- function(masses, mz_tol, intensity_weighted, intensities, bw_func, n = 512) {
   bandwidth <- 0.5 * mz_tol * bw_func(masses)
@@ -14,6 +21,15 @@ compute_densities <- function(masses, mz_tol, intensity_weighted, intensities, b
   return(all.mass.den)
 }
 
+#' Compute mass values based on kernel density estimation.
+#' @description
+#' This function computes the mass values by performing kernel density estimation on the given masses.
+#' It identifies the valleys in the density plot to determine the mass values.
+#' @param mz_tol The mass-to-charge ratio tolerance.
+#' @param masses A numeric vector of mass values.
+#' @param intensity_binned A numeric vector of binned intensity values corresponding to the masses.
+#' @param intensity_weighted A logical value indicating whether to weight the densities by intensities.
+#' @return A numeric vector of mass values corresponding to the valleys in the density plot.
 #' @export
 compute_mass_values <- function(mz_tol, masses, intensity_binned, intensity_weighted) {
   n <- 2^min(15, floor(log2(length(masses))) - 2)
@@ -33,6 +49,12 @@ compute_breaks <- function(mz_tol, masses, intensity_binned, intensity_weighted)
 }
 
 
+#' Increment pointers in a list.
+#' @description
+#' This function increments the values of `prof.pointer`, `height.pointer`, and `curr.label` in the provided list of pointers.
+#' @param pointers A list containing the pointers to be incremented.
+#' @param that.n An integer value to increment the `prof.pointer`.
+#' @return The updated list of pointers.
 #' @export
 increment_counter <- function(pointers, that.n){
   pointers$prof.pointer <- pointers$prof.pointer + that.n

R/plot.R

@@ -14,13 +14,33 @@ tolerance_plot <- function(x, y, exp_y, selected, main) {
   abline(v = x[selected], col = "blue")
 }
 
+#' Draw retention time normal peaks.
+#' @description
+#' This function draws the normal peaks for retention time data based on the provided parameters.
+#' @param x A numeric vector of retention time values.
+#' @param truth A numeric vector containing the parameters for the normal peaks:
+#' \itemize{
+#'   \item mean of the peak
+#'   \item standard deviation for the left side of the peak
+#'   \item standard deviation for the right side of the peak
+#'   \item scaling factor for the peak height
+#' }
 #' @export
 draw_rt_normal_peaks <- function(x, truth) {
   true.y1 <- dnorm(x[x < truth[1]], mean = truth[1], sd = truth[2]) * truth[2] * truth[4]
   true.y2 <- dnorm(x[x >= truth[1]], mean = truth[1], sd = truth[3]) * truth[3] * truth[4]
   lines(x, c(true.y1, true.y2), col = "green")
 }
 
+#' Plot raw profile histogram.
+#' @description
+#' This function plots various histograms and density plots for a given raw profile, including noise groups, selected groups, retention time range distribution, and signal presence distribution.
+#' @param raw.prof A list containing raw profile data, including height records and minimum count run.
+#' @param min_pres A numeric value indicating the minimum presence threshold.
+#' @param baseline.correct A numeric value for baseline correction. If NA, it will be computed automatically.
+#' @param baseline.correct.noise.percentile A numeric value indicating the percentile of noise group heights for baseline correction.
+#' @param mz_tol A numeric value for the mass-to-charge ratio tolerance.
+#' @param new.prof A list containing new profile data, including height records, time range records, and m/z presence records.
 #' @export
 plot_raw_profile_histogram <- function(raw.prof,
                                        min_pres,
@@ -80,6 +100,11 @@ plot_raw_profile_histogram <- function(raw.prof,
   )
 }
 
+#' Plot peak summary.
+#' @description
+#' This function plots a summary of peak characteristics, including m/z standard deviation, retention time standard deviation, and peak strength.
+#' @param feature_groups A list of data frames, where each data frame represents a group of features with m/z values.
+#' @param processed_features A data frame containing processed feature information with columns "sd1", "sd2", and "area".
 #' @export
 plot_peak_summary <- function(feature_groups, processed_features) {
   mz_sd <- compute_mz_sd(feature_groups)
@@ -92,6 +117,13 @@ plot_peak_summary <- function(feature_groups, processed_features) {
   hist(log10(processed_features[, "area"]), xlab = "peak strength (log scale)", ylab = "Frequency", main = "Peak strength distribution")
 }
 
+#' Plot retention time profile.
+#' @description
+#' This function plots the retention time profile, including the base curve, intensity, and fitted components.
+#' @param rt_profile A data frame containing the retention time profile with columns "base_curve" and "intensity".
+#' @param bw The bandwidth used for the kernel density estimation.
+#' @param fit A matrix containing the fitted components for the retention time profile.
+#' @param m A numeric vector of positions where vertical lines should be drawn.
 #' @export
 plot_rt_profile <- function(rt_profile, bw, fit, m) {
   plot(rt_profile[, "base_curve"], rt_profile[, "intensity"], cex = .1, main = paste("bw=", bw))
@@ -105,6 +137,18 @@ plot_rt_profile <- function(rt_profile, bw, fit, m) {
   }
 }
 
+#' Plot normalized mixture model with BIC.
+#' @description
+#' This function plots the data points and the fitted Gaussian mixture model components with different bandwidths.
+#' @param x A numeric vector of data points on the x-axis.
+#' @param y A numeric vector of data points on the y-axis.
+#' @param bw The bandwidth used for the kernel density estimation.
+#' @param aaa A matrix containing the parameters of the Gaussian mixture model components:
+#' \itemize{
+#'   \item mean of the Gaussian component
+#'   \item standard deviation of the Gaussian component
+#'   \item scaling factor for the Gaussian component
+#' }
 #' @export
 plot_normix_bic <- function(x, y, bw, aaa) {
   plot(x, y, cex = .1, main = paste("bw=", bw))
@@ -116,6 +160,14 @@ plot_normix_bic <- function(x, y, bw, aaa) {
   }
 }
 
+#' Draw retention time correction plot.
+#' @description
+#' This function draws a plot showing the retention time correction for extracted features.
+#' It plots the deviation of corrected retention times from the original retention times.
+#' @param colors A character vector of colors to use for plotting each sample. If NA, default colors are used.
+#' @param extracted_features A list of data frames, where each data frame contains the original retention times and m/z values of features.
+#' @param corrected_features A list of data frames, where each data frame contains the corrected retention times of features.
+#' @param rt_tol_relative A numeric value representing the relative retention time tolerance.
 #' @export
 draw_rt_correction_plot <- function(colors,
                                     extracted_features,

R/two.step.hybrid.R

@@ -102,6 +102,12 @@ wide_to_long_feature_table <- function(wide_table, sample_names) {
   return(long_features)
 }
 
+#' Extract column names matching a pattern.
+#' @description
+#' This function extracts the column names from a dataframe that contain a specified pattern.
+#' @param dataframe A dataframe from which to extract column names.
+#' @param pattern A character string containing the pattern to match in the column names.
+#' @return A character vector of column names that match the specified pattern.
 extract_pattern_colnames <- function(dataframe, pattern) {
   dataframe <- dplyr::select(dataframe, contains(pattern))
   return(colnames(dataframe))

R/utils.R

@@ -125,13 +125,21 @@ load_aligned_features <- function(metadata_file, intensities_file, rt_file, tol_
     return(result)
 }
 
+#' Calculate the span of a numeric vector.
+#' @description
+#' This function calculates the span (range) of a numeric vector, ignoring NA values.
+#' @param x A numeric vector.
+#' @return A numeric value representing the span of the vector.
 #' @export
 span <- function(x) {
     diff(range(x, na.rm = TRUE))
 }
 
+#' Compute standard deviation of m/z values for feature groups.
 #' @description
-#' Compute standard deviation of m/z values groupwise
+#' This function computes the standard deviation of m/z values for each group of features.
+#' @param feature_groups A list of data frames, where each data frame represents a group of features with m/z values.
+#' @return A numeric vector of standard deviations of m/z values for each feature group.
 #' @export
 compute_mz_sd <- function(feature_groups) {
     mz_sd <- c()
@@ -146,6 +154,10 @@ compute_mz_sd <- function(feature_groups) {
     return(mz_sd)
 }
 
+#' Get the number of available worker cores.
+#' @description
+#' This function determines the number of available worker cores, taking into account CRAN's limit on the number of cores.
+#' @return An integer representing the number of available worker cores.
 #' @export
 get_num_workers <- function() {
     # CRAN limits the number of cores available to packages to 2