R/get_QC_plots_and_stats.R

@@ -108,7 +108,8 @@ 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 +129,7 @@ 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. 
+
+DRUGSENS is a R-package that allows users to automatically analyze QuPath&trade's 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: `...`
@@ -9,9 +11,11 @@ This packge 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: