diff --git a/.Rbuildignore b/.Rbuildignore
index 8ef5bf9acaad61632c0e620b861b2b83fb08762f..0e96ecb5d0a412dddb2df1e6dd76eb5495d5756e 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -5,3 +5,7 @@
^\.github$
^LICENSE\.md$
^cran-comments\.md$
+^config_drugsens\.txt$
+^script_for_qupath\.txt$
+^assets$
+^CRAN-SUBMISSION$
diff --git a/.gitignore b/.gitignore
index 13e0c9533dbd47d6df773658aec0e9d4c9226084..2390fe4969104589e71914aa755eb6c5730b6a39 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,3 +8,5 @@
*.html
figures/**
temp/**
+.DS_Store
+*.txt
diff --git a/DESCRIPTION b/DESCRIPTION
index 9baf8b09c71eb902a8216d83afc60a285703ef99..9c045b5f1535b0b64349bad79910994f1f3728d3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,11 +1,11 @@
Package: drugsens
-Title: Automated Analysis of QuPath Output Data and Metadata Extraction
+Title: Automated Analysis of 'QuPath' Output Data and Metadata Extraction
Description: A comprehensive toolkit for analyzing microscopy data output from
- QuPath software. Provides functionality for automated data processing,
+ 'QuPath' software. Provides functionality for automated data processing,
metadata extraction, and statistical analysis of imaging results.
Designed to complement the STAR Protocol Protocol for quantifying drug
sensitivity in 3D patient-derived ovarian cancer models
- 10.1016/j.xpro.2024.103274.
+ <doi:10.1016/j.xpro.2024.103274>.
Version: 0.1.0
BugReports: https://git.scicore.unibas.ch/ovca-research/drugsens/-/issues
SystemRequirements: QuPathâ„¢ 4.0.0 or higher
diff --git a/R/change_data_format_to_longer.R b/R/change_data_format_to_longer.R
index c10a11e85c54cb1d0e28bab6aeb51cb7b0787a93..2de829482b5d12fde2398280c9fe4e7f5acc1104 100644
--- a/R/change_data_format_to_longer.R
+++ b/R/change_data_format_to_longer.R
@@ -1,6 +1,7 @@
#' Reformat the counts data in longer format
#' @description
#' This function gets the count data data.frame, that has a wider format and it returns a longer-formatted data.frame
+#' @title Data format changer
#' @importFrom tidyr pivot_longer
#' @importFrom dplyr select
#' @importFrom tidyselect any_of
@@ -11,6 +12,7 @@
#' @param unique_name_row_identifier String that indicates the unique identifier for each image, defaults as "filter_image"
#' @export
#' @examples
+#' \dontrun{
#' list_of_relabeling =list( "PathCellObject" = "onlyDAPIPositve",
#' "cCasp3" = "cCASP3", "E-Cadherin: cCASP3" = "E-Cadherin and cCASP3",
#' "EpCAM_E-Cadherin" = "E-Cadherin",
@@ -20,8 +22,7 @@
#' counts_dataframe <- make_count_dataframe(bind_data)
#' plotting_ready_dataframe <-
#' change_data_format_to_longer(counts_dataframe)
-
-# adding the image number so to identify the distribution
+#' }
# pivot_longer
change_data_format_to_longer <- function(.data,
diff --git a/R/data_binding.R b/R/data_binding.R
index 234725925f7e09ba076c4c550d0e2e7a5c3cf350..0f805b6314a98f1fd224079a041db8cc3953491d 100644
--- a/R/data_binding.R
+++ b/R/data_binding.R
@@ -1,19 +1,12 @@
# Get a list of all the files that are in a user-specified folder and get a list of full paths
+#' Internal utility functions for file handling
+#' @name utils_internal
#' @description
-#' This function lists the content of a selected folder either recursively or not
+#' This file contains internal utility functions for file handling and processing
#' @keywords internal
-#' @returns list
-#' @name "Name", "list_of_relabeling", "marker_positivity","marker_positivity_ratio", "x", "y"
#' @importFrom utils read.csv
#' @importFrom stats setNames
#' @import roxygen2
-#'
-
-# important for the scripts
-globalVariables(c(
- "Name", "list_of_relabeling", "marker_positivity",
- "marker_positivity_ratio", "x", "y"
-))
# list all the files
list_all_files <- function(define_path, extension, recursive_search) {
@@ -33,13 +26,14 @@ list_all_files <- function(define_path, extension, recursive_search) {
)
}
-# Helper function to read and process a single file
-#' @description
-#' This function returns a processed single file
+# Process a Single File
+#' @title Process a Single File
+#' @name process_file
+#' @description This function returns a processed single file
#' @param file_path Path to the file
#' @param extension String File extension to filter
#' @keywords internal
-#' @returns dataframe
+#' @return dataframe
process_file <- function(file_path,
# relabeling_map,
extension) {
@@ -85,27 +79,31 @@ process_file <- function(file_path,
}
#' Merge all the dataframes coming out from the QuPath
+#' @name data_binding
#' @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
+#' This function identifies string patterns in the dataset, fills the dataframe
+#' with that information, and combines all data into a single file
#' @import knitr
#' @importFrom stringr str_extract
-#' @return A `dataframe`/`tibble`.
#' @param path_to_the_projects_folder String/Path The path where the files coming out of QuPath are located
#' @param files_extension_to_look_for String The extension of the file outputted from QuPath, (default is "csv")
#' @param recursive_search Boolean, it defined the behavior of the file search, if recursive or not, (default is FALSE)
-#' @returns Returns a concatenated dataframe from all the files within the indicated one
+#' @param forcePath String defining an alternative path to the confic file
+#' @return A concatenated dataframe from all the files within the indicated path
#' @export
#' @examples
+#' \dontrun{
#' bind_data <- data_binding(path_to_the_projects_folder = system.file("extdata/to_merge/",
-#' package = "drugsens"))
-#' #This will return the dataframe of all the data in the folder
+#' package = "drugsens"))
+#'}
+
# Main function to bind data from multiple files
data_binding <- function(path_to_the_projects_folder,
files_extension_to_look_for = "csv",
- recursive_search = FALSE) {
+ recursive_search = FALSE,
+ forcePath = NULL) {
# run configuration file
- make_run_config()
+ make_run_config(forcePath = forcePath)
# Validate input parameters
if (!dir.exists(path_to_the_projects_folder)) {
diff --git a/R/generate_qu_path_script.R b/R/generate_qu_path_script.R
index 050661c3cf269e2149d1458fdce396a1b3c700aa..f006a2c632230f281f2b216eb85e00c636564af6 100644
--- a/R/generate_qu_path_script.R
+++ b/R/generate_qu_path_script.R
@@ -2,12 +2,12 @@
#' @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.
-#'
#' @return `script_for_qupath.txt` in local working directory.
-#'
#' @export
#' @examples
-#' generate_qupath_script()
+#' \dontrun{
+#' generate_qupath_script()
+#' }
generate_qupath_script <- function() {
write(
x = paste0('
diff --git a/R/get_QC_plots.R b/R/get_QC_plots.R
index 6f2403365665522255e6555cd4402483afb007ec..8a5336f3235507a92e5e8bf075c99aa550c3f70e 100644
--- a/R/get_QC_plots.R
+++ b/R/get_QC_plots.R
@@ -8,13 +8,15 @@
#' @param folder_name A string indicating the name of the folder where to save the plots in case that save_plots = TRUE
#' @param isolate_a_specific_patient A string indicating the patient name to isolate for single plot case (default is NULL)
#' @param x_plot_var A string indicating the treatment's full name for the QC plots (default is "Treatment_complete")
-#'
#' @import ggplot2
#' @import ggpubr
#' @importFrom dplyr filter
#' @return A `dataframe`/`tibble`.
-#' @example
-#' \dontrun{get_QC_plots(longer_format_dataframe, patient_column_name = "PID", save_plots = TRUE, folder_name = "figures")}
+#' @examples
+#' \dontrun{
+#' get_QC_plots(longer_format_dataframe, patient_column_name = "PID",
+#' save_plots = TRUE, folder_name = "figures")
+#' }
#' @export
get_QC_plots <- function(.data,
patient_column_name = "PID",
@@ -33,7 +35,9 @@ get_QC_plots <- function(.data,
QC_plot <- .data |>
dplyr::filter(.data[[patient_column_name]] == i) |>
- ggplot(aes(x = !!as.name(x_plot_var), y = marker_positivity_ratio, col = marker_positivity)) +
+ ggplot(aes(x = .data[[x_plot_var]],
+ y = .data$marker_positivity_ratio,
+ col = .data$marker_positivity)) +
geom_boxplot(
position = position_dodge(width = 1.0),
) +
diff --git a/R/get_QC_plots_and_stats.R b/R/get_QC_plots_and_stats.R
index cf1ebd2e1a9eeddf8226b472b71210b252485099..55719301decb751a1c99dbc3cc5ebf9f5544c2a7 100644
--- a/R/get_QC_plots_and_stats.R
+++ b/R/get_QC_plots_and_stats.R
@@ -16,14 +16,16 @@
#' @param p_height Integer, indicate the plot's height (default is 10 inches)
#' @param p_width Integer, indicate the plot's width (default is 10 inches)
#' @param drug_column_name String, indicate the column indicating the Drug/Treament (default is "Treatment")
-#'
#' @import ggplot2
#' @import ggpubr
#' @importFrom readr write_excel_csv
#' @importFrom dplyr filter
#' @return A `list`/`NULL`.
-#' @example
-#' \dontrun {qc <- get_QC_plots_parsed_merged_data(bind_data, save_plots = TRUE, save_list_of_plots = TRUE)}
+#' @examples
+#' \dontrun{
+#' qc <- get_QC_plots_parsed_merged_data(bind_data, save_plots = TRUE,
+#' save_list_of_plots = TRUE)
+#' }
#' @export
get_QC_plots_parsed_merged_data <- function(.data,
diff --git a/R/make_count_dataframe.R b/R/make_count_dataframe.R
index d0c783ad77e9efb8d1d62e3f585f5cd20389d879..2bc835856376b17266125e93ca74bfa9a46cbf24 100644
--- a/R/make_count_dataframe.R
+++ b/R/make_count_dataframe.R
@@ -8,12 +8,22 @@
#' @param 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"
#' @export
#' @examples
-#' bind_data <- data_binding(path_to_the_projects_folder = system.file("extdata/to_merge/", package = "drugsens"), files_extension_to_look_for = "csv")
+#' \dontrun{
+#' pkg_path <- system.file("extdata/to_merge/", package = "drugsens")
+#' bind_data <- data_binding(
+#' path_to_the_projects_folder = pkg_path,
+#' files_extension_to_look_for = "csv"
+#' )
#' counts_dataframe <- make_count_dataframe(bind_data)
-#' plotting_ready_dataframe <- change_data_format_to_longer(counts_dataframe)
-#' @example
-#' \dontrun{make_count_dataframe(data, name_of_the_markers_column = "Name", unique_name_row_identifier = "filter_image")}
-#' @return text file
+#' plotting_ready_dataframe <- change_data_format_to_longer(
+#' counts_dataframe
+#' )
+##' make_count_dataframe(
+#' data,
+#' name_of_the_markers_column = "Name",
+#' unique_name_row_identifier = "filter_image"
+#' )
+#' }
# adding the image number so to identify the distribution
make_count_dataframe <- function(.data, unique_name_row_identifier = "filter_image",
diff --git a/R/make_run_config.R b/R/make_run_config.R
index 232cdc4e136c51027728e7990ee57c7884e6f176..ab009a74c835fe90931b0d7eb36972c3eb8dcd61 100644
--- a/R/make_run_config.R
+++ b/R/make_run_config.R
@@ -1,3 +1,5 @@
+# In make_run_config.R:
+
#' Generates and use a config txt file
#' @description
#' When this function run the first time, it will generated a config.txt file in the user working directory.
@@ -7,16 +9,18 @@
#' @param forcePath String, Define a custom path for the config file
#' @export
#' @return A `dataframe`/`tibble`.
-#' @example
-#' \dontrun {make_run_config()}
+#' @examples
+#' \dontrun{
+#' make_run_config()
+#' }
make_run_config <- function(overwrite_config = FALSE, forcePath = NULL) {
+ currentPath <- if (is.null(forcePath)) getwd() else forcePath
+ config_file <- file.path(currentPath, "config_drugsens.txt")
- if (is.null(forcePath)) currentPath <- getwd() else currentPath <- forcePath
-
- if (file.exists("config_drugsens.txt")) {
+ if (file.exists(config_file)) {
tryCatch(
expr = {
- source("config_drugsens.txt", local = FALSE)
+ source(config_file, local = FALSE)
},
error = function(error) {
message("drugsens could not load the 'config.txt' file.
@@ -26,13 +30,9 @@ make_run_config <- function(overwrite_config = FALSE, forcePath = NULL) {
run_config to veryfy that the data was correctly read")
}
)
- } else if (overwrite_config){
- message("Overwriting config_drugsens.txt")
+ } else if (overwrite_config) {
write(
- x =
- (
- '
- # List of markers to relabel
+ x = '# List of markers to relabel
list_of_relabeling =
list(
"PathCellObject" = "onlyDAPIPositve",
@@ -40,17 +40,12 @@ make_run_config <- function(overwrite_config = FALSE, forcePath = NULL) {
"E-Cadherin: cCASP3" = "E-Cadherin and cCASP3",
"EpCAM_E-Cadherin" = "E-Cadherin",
"EpCAM_E-Cadherin and cCASP3" = "E-Cadherin and cCASP3"
- )'
- ),
- file = paste0(path.expand(currentPath), "/config_drugsens.txt")
+ )',
+ file = config_file
)
- message("config_drugsens.txt has been overwritten correctly.")
} else {
write(
- x =
- (
- '
- # List of markers to relabel
+ x = '# List of markers to relabel
list_of_relabeling =
list(
"PathCellObject" = "onlyDAPIPositve",
@@ -58,9 +53,8 @@ make_run_config <- function(overwrite_config = FALSE, forcePath = NULL) {
"E-Cadherin: cCASP3" = "E-Cadherin and cCASP3",
"EpCAM_E-Cadherin" = "E-Cadherin",
"EpCAM_E-Cadherin and cCASP3" = "E-Cadherin and cCASP3"
- )'
- ),
- file = paste0(path.expand(currentPath), "/config_drugsens.txt")
+ )',
+ file = config_file
)
}
}
diff --git a/R/parsers.R b/R/parsers.R
index ed40c09643b7eaa318bfdc94c030f1e8d58149d8..bc0153f8e4d2c059854c66fff23e8ee60768cfd3 100644
--- a/R/parsers.R
+++ b/R/parsers.R
@@ -9,10 +9,13 @@
#' @return A `dataframe`/`tibble`.
#' @param .data dataframe with parsed metadata
#' @examples
-#' input_data <- data.frame(Image = "B516_Ascites_2023-11-25_DOC2020-12-14_dmso_rep_Ecad_cCasp3_(series 01).tif")
-#' test <- drugsens:::string_parsing(input_data)
-#' @example
-#' \dontrun {data.parsed <- string_parsing(.data)}
+#' input_data <- data.frame(
+#' Image = "B516_Ascites_2023-11-25_DOC2020-12-14_dmso_rep_Ecad_cCasp3_(series 01).tif"
+#' )
+#' test <- drugsens:::string_parsing(input_data)
+#' \dontrun{
+#' data.parsed <- string_parsing(.data)
+#' }
# Main function to bind data from multiple files
string_parsing <- function(.data) {
diff --git a/R/zzz.R b/R/zzz.R
new file mode 100644
index 0000000000000000000000000000000000000000..6f2304e156759de9ccdf4ac309dcf1a2537e234c
--- /dev/null
+++ b/R/zzz.R
@@ -0,0 +1,10 @@
+.onLoad <- function(libname, pkgname) {
+ utils::globalVariables(c(
+ "list_of_relabeling",
+ "marker_positivity_ratio",
+ "marker_positivity",
+ "x",
+ "y",
+ "Name"
+ ))
+}
diff --git a/README.md b/README.md
index 7fd35d71d49f16084343219e3911e5e5bd914afd..e2e67f46832eefd5af7b32ae297cfcf1fa93d16b 100644
--- a/README.md
+++ b/README.md
@@ -208,7 +208,7 @@ In this code snippets we show an example of mock data `unique(bind_data$PID)` wi
> âš ï¸ **WARNING**: As long as you keep the formatting as the above examples.
The dates should also be in the format **yyy-mm-dd**. For the combinations of two drugs they should be written together with each of the different drug capilized (**C**arboplatin**P**aclitaxel) and the rest lowercased letters.
-For example **CarboplatinPaclitaxel_100_uM_10_nM**. This indicates a drug combination of Carboplatin 100_uM and Paclitaxel 10_nM. Each drug amount and each unit should always be separated by `_`. The first 100_uM belongs to the Carboplatin and the 10_nM belongs to the Paclitaxel. Those constrains are due to the parsing of the strings into useful metadata. If some of the data is not present, you can use a `.` separated by `_`. If you need additional data parsing, please let us know by filing an issue on GitLab [GitLab Issue]("https://git.scicore.unibas.ch/ovca-research/drugsens/-/issues").
+For example **CarboplatinPaclitaxel_100_uM_10_nM**. This indicates a drug combination of Carboplatin 100_uM and Paclitaxel 10_nM. Each drug amount and each unit should always be separated by `_`. The first 100_uM belongs to the Carboplatin and the 10_nM belongs to the Paclitaxel. Those constrains are due to the parsing of the strings into useful metadata. If some of the data is not present, you can use a `.` separated by `_`. If you need additional data parsing, please let us know by filing an issue on GitLab https://git.scicore.unibas.ch/ovca-research/drugsens/-/issues.
### Counting the number of positiive cells for each marker in every image
This function will take the previous step's generated dataframe and it will counts image by image (sum the markers of every stack) for every sample the number of marker occurrences.
@@ -386,6 +386,6 @@ Renv will automatically activate and install the necessary packages as specified
</details>
### Reporting Issues
-If you encounter any bugs or have suggestions for improvements, please file an issue using our [GitLab Issue]("https://git.scicore.unibas.ch/ovca-research/drugsens/-/issues"). Be sure to include as much information as possible to help us understand and address the issue.
-
+If you encounter any bugs or have suggestions for improvements, please file an issue using our **GitLab Issue:** https://git.scicore.unibas.ch/ovca-research/drugsens/-/issues. Be sure to include as much information as possible to help us understand and address the issue.
+**BugReports:** https://git.scicore.unibas.ch/ovca-research/drugsens/-/issues
Please make sure to file the issue in the GitLab repo as this one in GitHub is a forward-only mirror repo.
diff --git a/man/change_data_format_to_longer.Rd b/man/change_data_format_to_longer.Rd
index 93849cb4fc435e5def2f8b9c204a974b83ac1a48..93a2d8353a5b0aace9ea37f17319dd70d9605b78 100644
--- a/man/change_data_format_to_longer.Rd
+++ b/man/change_data_format_to_longer.Rd
@@ -2,7 +2,7 @@
% 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}
+\title{Data format changer}
\usage{
change_data_format_to_longer(
.data,
@@ -26,7 +26,11 @@ 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
}
+\details{
+Reformat the counts data in longer format
+}
\examples{
+\dontrun{
list_of_relabeling =list( "PathCellObject" = "onlyDAPIPositve",
"cCasp3" = "cCASP3", "E-Cadherin: cCASP3" = "E-Cadherin and cCASP3",
"EpCAM_E-Cadherin" = "E-Cadherin",
@@ -37,3 +41,4 @@ counts_dataframe <- make_count_dataframe(bind_data)
plotting_ready_dataframe <-
change_data_format_to_longer(counts_dataframe)
}
+}
diff --git a/man/data_binding.Rd b/man/data_binding.Rd
index 1f1ebcc8d69cb18850cad87e5fb2de9571276439..13fd6320ea24fd44a9952e796f177f48e6c9e805 100644
--- a/man/data_binding.Rd
+++ b/man/data_binding.Rd
@@ -7,7 +7,8 @@
data_binding(
path_to_the_projects_folder,
files_extension_to_look_for = "csv",
- recursive_search = FALSE
+ recursive_search = FALSE,
+ forcePath = NULL
)
}
\arguments{
@@ -16,18 +17,19 @@ data_binding(
\item{files_extension_to_look_for}{String The extension of the file outputted from QuPath, (default is "csv")}
\item{recursive_search}{Boolean, it defined the behavior of the file search, if recursive or not, (default is FALSE)}
+
+\item{forcePath}{String defining an alternative path to the confic file}
}
\value{
-A \code{dataframe}/\code{tibble}.
-
-Returns a concatenated dataframe from all the files within the indicated one
+A concatenated dataframe from all the files within the indicated path
}
\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
+This function identifies string patterns in the dataset, fills the dataframe
+with that information, and combines all data into a single file
}
\examples{
+\dontrun{
bind_data <- data_binding(path_to_the_projects_folder = system.file("extdata/to_merge/",
-package = "drugsens"))
-#This will return the dataframe of all the data in the folder
+ package = "drugsens"))
+}
}
diff --git a/man/generate_qupath_script.Rd b/man/generate_qupath_script.Rd
index 4e32a38406518db57c72c09a4476cfe6259c88d5..89b18160e079a24ebf48d517e7b513df0efa10ce 100644
--- a/man/generate_qupath_script.Rd
+++ b/man/generate_qupath_script.Rd
@@ -14,5 +14,7 @@ Generate a useful script to consistently save the output data from QuPath in .cs
followed during the package development.
}
\examples{
-generate_qupath_script()
+\dontrun{
+ generate_qupath_script()
+}
}
diff --git a/man/get_QC_plots.Rd b/man/get_QC_plots.Rd
index 27070aa5733ac8a41bd3a8aeb0a6d5621258adc5..0b4825e4aded1c593f206b2172c7f3b463ef1b1d 100644
--- a/man/get_QC_plots.Rd
+++ b/man/get_QC_plots.Rd
@@ -35,3 +35,9 @@ A \code{dataframe}/\code{tibble}.
\description{
Plot data to visualize immediate trends
}
+\examples{
+\dontrun{
+ get_QC_plots(longer_format_dataframe, patient_column_name = "PID",
+ save_plots = TRUE, folder_name = "figures")
+}
+}
diff --git a/man/get_QC_plots_parsed_merged_data.Rd b/man/get_QC_plots_parsed_merged_data.Rd
index 72eac55481806a9cd2b7f936b0cdfca49fa98628..221cc7ebc3b0a5e14b4ddd6e82a8a27f17132047 100644
--- a/man/get_QC_plots_parsed_merged_data.Rd
+++ b/man/get_QC_plots_parsed_merged_data.Rd
@@ -53,3 +53,9 @@ A \code{list}/\code{NULL}.
\description{
This plot can show trends within the dataset and run some basic statistics.
}
+\examples{
+\dontrun{
+ qc <- get_QC_plots_parsed_merged_data(bind_data, save_plots = TRUE,
+ save_list_of_plots = TRUE)
+}
+}
diff --git a/man/make_count_dataframe.Rd b/man/make_count_dataframe.Rd
index b11831954502f1f90097b829d5e4662c381d58ec..256353e95a1e776504baacad5edf2d833426549a 100644
--- a/man/make_count_dataframe.Rd
+++ b/man/make_count_dataframe.Rd
@@ -19,14 +19,25 @@ make_count_dataframe(
}
\value{
A \code{dataframe}/\code{tibble}.
-
-text file
}
\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
}
\examples{
-bind_data <- data_binding(path_to_the_projects_folder = system.file("extdata/to_merge/", package = "drugsens"), files_extension_to_look_for = "csv")
+\dontrun{
+pkg_path <- system.file("extdata/to_merge/", package = "drugsens")
+bind_data <- data_binding(
+ path_to_the_projects_folder = pkg_path,
+ files_extension_to_look_for = "csv"
+)
counts_dataframe <- make_count_dataframe(bind_data)
-plotting_ready_dataframe <- change_data_format_to_longer(counts_dataframe)
+plotting_ready_dataframe <- change_data_format_to_longer(
+ counts_dataframe
+)
+ make_count_dataframe(
+ data,
+ name_of_the_markers_column = "Name",
+ unique_name_row_identifier = "filter_image"
+ )
+}
}
diff --git a/man/make_run_config.Rd b/man/make_run_config.Rd
index 40042efd9a435e075fff06bf6c48cdba9681bb77..a56cf8e6b06a21416816cd92a451ab007c82f9e2 100644
--- a/man/make_run_config.Rd
+++ b/man/make_run_config.Rd
@@ -19,3 +19,8 @@ When this function run the first time, it will generated a config.txt file in th
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.
}
+\examples{
+\dontrun{
+ make_run_config()
+}
+}
diff --git a/man/process_file.Rd b/man/process_file.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..db4b16b31168fb4e22a981b47e8215d64870874b
--- /dev/null
+++ b/man/process_file.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_binding.R
+\name{process_file}
+\alias{process_file}
+\title{Process a Single File}
+\usage{
+process_file(file_path, extension)
+}
+\arguments{
+\item{file_path}{Path to the file}
+
+\item{extension}{String File extension to filter}
+}
+\value{
+dataframe
+}
+\description{
+This function returns a processed single file
+}
+\keyword{internal}
diff --git a/man/string_parsing.Rd b/man/string_parsing.Rd
index c6d8fc1bbfb217bd90fb88890fc52f87af41bd94..e6b8843a3ce9e4db1e0a479153d663c645bcc800 100644
--- a/man/string_parsing.Rd
+++ b/man/string_parsing.Rd
@@ -17,6 +17,11 @@ This function will parse the data from the Image name and will return the metada
The metadata will be then associated to the count file as well
}
\examples{
- input_data <- data.frame(Image = "B516_Ascites_2023-11-25_DOC2020-12-14_dmso_rep_Ecad_cCasp3_(series 01).tif")
- test <- drugsens:::string_parsing(input_data)
+input_data <- data.frame(
+ Image = "B516_Ascites_2023-11-25_DOC2020-12-14_dmso_rep_Ecad_cCasp3_(series 01).tif"
+)
+test <- drugsens:::string_parsing(input_data)
+\dontrun{
+ data.parsed <- string_parsing(.data)
+}
}
diff --git a/man/utils_internal.Rd b/man/utils_internal.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..a0dfbbe295b7d9d142f5cf007ee36d274c91d390
--- /dev/null
+++ b/man/utils_internal.Rd
@@ -0,0 +1,13 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_binding.R
+\name{utils_internal}
+\alias{utils_internal}
+\alias{list_all_files}
+\title{Internal utility functions for file handling}
+\usage{
+list_all_files(define_path, extension, recursive_search)
+}
+\description{
+This file contains internal utility functions for file handling and processing
+}
+\keyword{internal}
diff --git a/tests/testthat/test_cases.R b/tests/testthat/test_cases.R
index 06d85a8be5e4d1b74e544cd9c88cae0019406b83..bb105ab40b659ca354c4b7d91dac2b4bfff1667e 100644
--- a/tests/testthat/test_cases.R
+++ b/tests/testthat/test_cases.R
@@ -39,10 +39,13 @@ test_that("list_all_files returns correct file paths", {
})
-test_that("Check that the config.txt is made and that it can be read", {
- expect_silent(make_run_config())
- expect_silent(make_run_config())
- expect_true(file.exists(path.expand(path = paste0(getwd(), "/config_drugsens.txt"))))
+test_that("Config creation and reading works", {
+ temp_dir <- tempdir()
+ on.exit(unlink(file.path(temp_dir, "config_drugsens.txt")))
+
+ make_run_config(forcePath = temp_dir)
+ make_run_config(forcePath = temp_dir)
+ expect_true(file.exists(file.path(temp_dir, "config_drugsens.txt")))
expect_true(exists("list_of_relabeling"))
})
@@ -62,6 +65,7 @@ test_that("Config file was there and removed correctly", {
expect_silent( file.remove(path.expand(paste0(getwd(), "/config_drugsens.txt"))) )
})
+
test_that("The parsing is working", {
input_data <- data.frame(Image = "PID1_Tissue1_2024-02-13_DOC2024.02.13_TreatmentRana_10_uM_15_nm_Replica_(series.10)")
expected_output <- data.frame(