Init DRUGSENS

man/change_data_format_to_longer.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/change_data_format_to_longer.R
+\name{change_data_format_to_longer}
+\alias{change_data_format_to_longer}
+\title{Reformat the counts data in longer format}
+\usage{
+change_data_format_to_longer(
+  .data,
+  pattern_column_markers = "_ratio_of_total_cells",
+  unique_name_row_identifier = "filter_image",
+  additional_columns = TRUE
+)
+}
+\arguments{
+\item{.data}{The markers count dataframe that is coming from the processing of the microscopy data}
+
+\item{pattern_column_markers}{The markers' pattern name to obtain the column with ratios of the markers (it defaults to "_ratio_of_total_cells")}
+
+\item{unique_name_row_identifier}{String that indicates the unique identifier for each image, defaults as "filter_image"}
+
+\item{additional_columns}{columns that can be additionally added to the longer formatted data.frame, "Defaults as c("Treatment", "PID", "Image_number", "Tissue", "Concentration", "DOC")"}
+}
+\value{
+A \code{dataframe}/\code{tibble}.
+}
+\description{
+This function gets the count data data.frame, that has a wider format and it returns a longer-formatted data.frame
+}

man/data_binding.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_binding.R
+\name{data_binding}
+\alias{data_binding}
+\title{Merge all the dataframes coming out from the QuPath}
+\usage{
+data_binding(
+  path_to_the_projects_folder,
+  files_extension_to_look_for,
+  recursive_search = FALSE
+)
+}
+\arguments{
+\item{path_to_the_projects_folder}{The path where the files coming out of QuPath are located}
+
+\item{files_extension_to_look_for}{The extension of the file outputted from QuPath}
+
+\item{recursive_search}{Boolean, it defined the behavior of the file search, if recursive or not, (default is FALSE)}
+}
+\value{
+A \code{dataframe}/\code{tibble}.
+}
+\description{
+This function try to guess the string patterns that are in the dataset and then fill the dataframe
+with that information. Finally the data is combined and combined them into one file
+}

man/generate_qupath_script.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/generate_qu_path_script.R
+\name{generate_qupath_script}
+\alias{generate_qupath_script}
+\title{Generate the groovy script used for the analysis}
+\usage{
+generate_qupath_script()
+}
+\value{
+\verb{script_for_qupath.txt in local dir}.
+}
+\description{
+Generate a useful script to consistently save the output data from QuPath in .csv format following the naming conventions
+followed during the package development.
+}

man/get_QC_plots.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_QC_plots.R
+\name{get_QC_plots}
+\alias{get_QC_plots}
+\title{Plot some QC plots to define that everything ran correctly}
+\usage{
+get_QC_plots(
+  .data,
+  patient_column_name = "PID",
+  colors = c("darkgreen", "red", "orange", "pink"),
+  save_plots = FALSE,
+  folder_name = "figures",
+  x_plot_var = "Treatment_complete",
+  isolate_a_specific_patient = NULL
+)
+}
+\arguments{
+\item{.data}{The preprocessed data (after running make_count_dataframe() and change_data_format_to_longer()) merged data.frame that should be visualized}
+
+\item{patient_column_name}{The PID's column name in the merged data.frame (defaults to "PID")}
+
+\item{colors}{A list of colors to supply to personalize the plot, as default 4 colors c("dark green", "red", "orange", "pink")}
+
+\item{save_plots}{A Boolean value indicating if the plots should be saved or not, TRUE for saving in the current working directory, FALSE to not. Default is FALSE}
+
+\item{folder_name}{A string indicating the name of the folder where to save the plots in case that save_plots = TRUE}
+
+\item{x_plot_var}{A string indicating the treatment's full name for the QC plots (default is "Treatment_complete")}
+
+\item{isolate_a_specific_patient}{A string indicating the patient name to isolate for single plot case (default is NULL)}
+}
+\value{
+A \code{dataframe}/\code{tibble}.
+}
+\description{
+Plot data to visualize immediate trends
+}

man/make_count_dataframe.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/make_count_dataframe.R
+\name{make_count_dataframe}
+\alias{make_count_dataframe}
+\title{Count the main marker expression}
+\usage{
+make_count_dataframe(
+  .data,
+  unique_name_row_identifier = "filter_image",
+  name_of_the_markers_column = "Name"
+)
+}
+\arguments{
+\item{.data}{The dataframe that is coming from the processing of the microscopy data}
+
+\item{unique_name_row_identifier}{The name of the column of the .data where the unique name can be used to counts (it defaults to "filter_image")}
+
+\item{name_of_the_markers_column}{The name of the column of the .data where the marker names are expressed (ie E-Caderin, DAPI), "Defaults as Name"}
+}
+\value{
+A \code{dataframe}/\code{tibble}.
+}
+\description{
+This function counts every single marker present in the "Name" column of the data.frame and return a dataframe of the counts per marker
+}

man/make_run_config.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/make_run_config.R
+\name{make_run_config}
+\alias{make_run_config}
+\title{Generates and use a config txt file}
+\usage{
+make_run_config()
+}
+\value{
+A \code{dataframe}/\code{tibble}.
+}
+\description{
+When this function run the first time, it will generated a config.txt file in the user working directory.
+It will import the data config file into the use environment. This data will be used to change the column names
+of the imported dataset and change the name of the markers that is often incorrectly exported.
+}

renv/.gitignore

+library/
+local/
+cellar/
+lock/
+python/
+sandbox/
+staging/

tests/testthat.R

+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(DRUGSENS)
+
+test_check("DRUGSENS")

tests/testthat/test_cases.R

+test_that("Verify that the internal file in to_merge examples in exdata are available", {
+  list_files_exdata <- system.file("extdata/to_merge/", package = "DRUGSENS") |> list.files()
+  expect_true(length(list_files_exdata) > 3 )
+})
+
+test_that("Verify that the internal file examples in exdata merged are available", {
+  list_files_exdata <- system.file("extdata/merged/", package = "DRUGSENS") |> list.files()
+  expect_true(length(list_files_exdata) >= 1 )
+})
+
+test_that("list_all_files returns correct file paths", {
+  # Setup: Create temporary files and directory
+  temp_dir <- tempdir()
+  file.create(file.path(temp_dir, "file1.csv"))
+  file.create(file.path(temp_dir, "file2.csv"))
+  file.create(file.path(temp_dir, "file3.txt"))
+  file.create(file.path(temp_dir, "file4.tsv"))
+
+  # Test 1
+  files_list <- list_all_files(define_path = temp_dir, extension = "\\.csv$",
+                               recursive_search = T)
+  expect_length(files_list, 2)
+  expect_true(all(grepl("file1.csv|file2.csv", files_list)))
+
+  # Test 2
+  files_list <- list_all_files(define_path = temp_dir, extension = "\\.txt$",
+                               recursive_search = T)
+  expect_length(files_list, 1)
+  expect_true(all(grepl("file3.txt", files_list)))
+
+  # Test 3
+  files_list <- list_all_files(define_path = temp_dir, extension = "\\.tsv$",
+                               recursive_search = T)
+  expect_length(files_list, 1)
+  expect_true(all(grepl("file4.tsv", files_list)))
+
+  # remove the dir
+  unlink(temp_dir, recursive = TRUE)
+
+})
+
+test_that("Check that the config.txt is made and can be read", {
+  expect_silent(make_run_config())
+  expect_silent(make_run_config())
+  expect_true(exists("list_of_relabeling"))
+})
+
+# WIP add for the regex in preprocessing