diff --git a/R/get_QC_plots_and_stats.R b/R/get_QC_plots_and_stats.R index 7872515943dbff57c0f35e1bddc24f63b28acef1..e6825ccb81137aefc118378e011cda88dcfd0342 100644 --- a/R/get_QC_plots_and_stats.R +++ b/R/get_QC_plots_and_stats.R @@ -108,7 +108,7 @@ 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, diff --git a/README.md b/README.md index 837bb55a605aaadeb7931bfb93d6cddbaa35aa52..f5ce505c50893f6d2ddb3ecf1f5d04db6eb73485 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@  # 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™ 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: `...` @@ -9,7 +9,7 @@ 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 ```