diff --git a/R/get_QC_plots_and_stats.R b/R/get_QC_plots_and_stats.R index 7872515943dbff57c0f35e1bddc24f63b28acef1..a2977fedae0cda566fec0bbd17ff4988277e9fec 100644 --- a/R/get_QC_plots_and_stats.R +++ b/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, diff --git a/README.md b/README.md index 837bb55a605aaadeb7931bfb93d6cddbaa35aa52..63f5c684f30d966e4113b39a7c1e2d834a4f060f 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,8 @@  # 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™'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 +10,11 @@ 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: @@ -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.