Fix typos

R/change_data_format_to_longer.R

@@ -43,12 +43,8 @@ change_data_format_to_longer <- function(.data,
 
   if (length(col_names_of_markers) < 1) stop(paste0("Failed to find pattern: ", pattern_column_markers, " in the columnames"))
 
-  # if (!all(additional_columns_to_use %in% colnames(.data))) stop(paste0('One or more of the following columnames:
-  #                                                    c(Treatment", "PID", "Image_number", "Tissue", "Concentration", "DOC") could not be found.
-  #                                                    Please check the names of your data.frame and/or provide your selection'),
-  #                                                    "Those are the colnames found in the input data: ",
-  #                                                    colnames(.data))
   if (!"Image_number" %in% additional_columns_to_use) stop("Image_number has to be in the dataframe.")
+
   if (!"Treatment_complete" %in% additional_columns_to_use) stop("Treatment_complete has to be in the dataframe.")
 
 

R/get_QC_plots_and_stats.R

@@ -59,7 +59,6 @@ get_QC_plots_parsed_merged_data <- function(.data,
     subset_data <- .data[.data[[PID_column_name]] == pid, ]
 
     for (i in list_of_columns_to_plot) {
-      # if (!isolate_specific_drug %in% subset_data[[drug_column_name]] |> unique()) stop("ERROR: The `isolate_specific_drug` is not included in the name of the availble treaments.")
       if (!is.null(isolate_specific_drug)) subset_data <- subset_data[subset_data[[drug_column_name]] %in% isolate_specific_drug, ]
 
       if (nrow(subset_data) < 1) {
@@ -108,7 +107,8 @@ get_QC_plots_parsed_merged_data <- function(.data,
 
       if (save_plots) {
         if (save_plots_in_patient_specific_subfolders) {
-          if (!dir.exists(paste0(saving_plots_folder, "/", pid))) dir.create(paste0(saving_plots_folder, "/", pid))
+
+          if (!dir.exists(paste0(saving_plots_folder, "/", pid))) dir.create(paste0(saving_plots_folder, "/", pid), showWarnings = F, recursive = T)
           ggsave(
             plot = p,
             filename = paste0(
@@ -128,7 +128,7 @@ get_QC_plots_parsed_merged_data <- function(.data,
           )
         } else {
           # Saving plots in .pdf at 600 dpi
-          if (!dir.exists(saving_plots_folder)) dir.create(saving_plots_folder)
+          if (!dir.exists(saving_plots_folder)) dir.create(saving_plots_folder, showWarnings = F, recursive = T)
           ggsave(
             plot = p,
             width = p_width,

README.md

 ![](https://img.shields.io/badge/R-%3E%3D%204.0.0-blue)
 
 # Overview
-DRUGSENS is a R-package tha allow users to automatically analyze QuPath™ output data from imaging analysis. 
-Here we include a QuPath™ script to run reproducible QuPath™-based image analysis, and some examples on how DRUGSENS can be used. For more detailed examples of QuPath™ scripting please refer to [QuPath™'s Documentation](https://qupath.readthedocs.io/en/stable/). 
-This script should be placed into scripts within QuPath™. We tested this code to a previous version of QuPath&trade.
-This packge is complementary to the STAR protocol: `...`
+
+DRUGSENS is a R-package that allows users to automatically analyze QuPath™'s output data from imaging analysis. 
+Here we include a QuPath™ script (the same that we regularly use) to run reproducible QuPath™-based image analysis, and some examples on how DRUGSENS can be used. For more detailed examples of QuPath™ scripting and usage please refer to [QuPath™'s Documentation](https://qupath.readthedocs.io/en/stable/). 
+This script should be placed into scripts manager within QuPath™. We tested this code with previous versions of QuPath™, but new versions should also be compatible.
+This package is complementary to the STAR protocol: `...`
 
 # Installation
 
 ``` r
-devtools::install_gitlab("https://git.scicore.unibas.ch/ovca-research/drugsens")
+devtools::install_git("https://git.scicore.unibas.ch/ovca-research/drugsens")
+
 # OR
-devtools::install_github("https://github.com/flalom/drugsens") # this is the mirroring repo of the gitlab
+
+devtools::install_github("https://github.com/flalom/drugsens") # this is the GitLab's mirroring repo
 ```
 
 `devtools` is required to install DRUGSENS. If `devtools` is not installed yet you can install it with:
@@ -313,4 +316,4 @@ Renv will automatically activate and install the necessary packages as specified
 ### 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.
 
-Please make sure to file the issue in gitlab as the GitHub is a mirror repo.
+Please make sure to file the issue in the GitLab repo as this one in GitHub is a forward-only mirror repo.