From 07223ef1366ec98c140401a3d50bf4426226a12d Mon Sep 17 00:00:00 2001
From: Konrad1991 <konrad_kraemer@yahoo.de>
Date: Mon, 22 Apr 2024 10:11:49 +0200
Subject: [PATCH] fixed error in removeOutlier function

---
 Dockerfile               |  4 +++-
 MTT/DESCRIPTION          |  2 +-
 MTT/NAMESPACE            |  1 +
 MTT/R/import.R           | 11 +++++++----
 MTT/man/removeOutlier.Rd | 18 ++++++++++++++++++
 build_and_run.sh         |  0
 installMTT.R             |  2 ++
 push2docker.sh           |  5 +++--
 run.sh                   |  5 +++--
 shinychem.Rproj          | 13 -------------
 10 files changed, 38 insertions(+), 23 deletions(-)
 create mode 100644 MTT/man/removeOutlier.Rd
 mode change 100644 => 100755 build_and_run.sh
 create mode 100644 installMTT.R
 mode change 100644 => 100755 push2docker.sh
 mode change 100644 => 100755 run.sh
 delete mode 100644 shinychem.Rproj

diff --git a/Dockerfile b/Dockerfile
index 40f1fe7..8da7ab6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -43,7 +43,9 @@ RUN install2.r --error --skipinstalled \
     ggpmisc \
     jose \
     R6 \
-    patchwork
+    patchwork \
+    cowplot \
+    quarto
     
 USER shiny
 COPY ./app/ ./myapp
diff --git a/MTT/DESCRIPTION b/MTT/DESCRIPTION
index a9fc66e..2eae7ce 100644
--- a/MTT/DESCRIPTION
+++ b/MTT/DESCRIPTION
@@ -8,5 +8,5 @@ Maintainer: <konrad_kraemer@kit.edu>
 Description: Import xml files from platereader. Calculation of LD50. Creating boxplots of raw data and the curves used for calculation of LD50.
 License: GPL-2
 Imports: tidyr, ggplot2, drc, R6, quarto, openxlsx, cowplot, gridExtra
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Encoding: UTF-8
diff --git a/MTT/NAMESPACE b/MTT/NAMESPACE
index 73145e8..b8d8eed 100644
--- a/MTT/NAMESPACE
+++ b/MTT/NAMESPACE
@@ -3,6 +3,7 @@
 export(XML2DF)
 export(ic50)
 export(import)
+export(removeOutlier)
 export(report_pdf)
 export(save)
 import(drc)
diff --git a/MTT/R/import.R b/MTT/R/import.R
index 17a6d5b..1aa7106 100644
--- a/MTT/R/import.R
+++ b/MTT/R/import.R
@@ -137,10 +137,12 @@ import <- function(path, names = names_default(), conc = conc_default()) {
 #' @param l a list containing column indices which defines the different groups
 #' @param dep the column index which defines the dependent variable
 removeOutlier <- function(df, l, dep) {
-  int <- sapply(seq_along(1:length(df)), function(x) {
-    paste0(df[, l], collapse = "_")
-  })
+  ps <- function(a, b) {
+    paste0(a, "_", b)
+  }
+  int <- Reduce(ps, as.list(df[, l]))
   intUnique <- unique(int)
+  
   dfor <- lapply(intUnique, function(x) {
    temp <- df[int == x, ]
    bs <- boxplot.stats(temp$abs)
@@ -148,5 +150,6 @@ removeOutlier <- function(df, l, dep) {
    temp[temp$abs %in% bs$out, "abs"] <- NA
    return(temp)
   })
-  do.call(rbind, dfor)
+  df <- do.call(rbind, dfor)
+  df[!is.na(df$abs), ]
 }
diff --git a/MTT/man/removeOutlier.Rd b/MTT/man/removeOutlier.Rd
new file mode 100644
index 0000000..f08eb72
--- /dev/null
+++ b/MTT/man/removeOutlier.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/import.R
+\name{removeOutlier}
+\alias{removeOutlier}
+\title{remove outliers}
+\usage{
+removeOutlier(df, l, dep)
+}
+\arguments{
+\item{df}{a data.frame from which the outliers should be removed}
+
+\item{l}{a list containing column indices which defines the different groups}
+
+\item{dep}{the column index which defines the dependent variable}
+}
+\description{
+remove outliers
+}
diff --git a/build_and_run.sh b/build_and_run.sh
old mode 100644
new mode 100755
diff --git a/installMTT.R b/installMTT.R
new file mode 100644
index 0000000..866fb8a
--- /dev/null
+++ b/installMTT.R
@@ -0,0 +1,2 @@
+install.packages("/home/konrad/Documents/GitHub/RProjects/shinychem/MTT",
+                 type = "source", repos = NULL)
diff --git a/push2docker.sh b/push2docker.sh
old mode 100644
new mode 100755
index d634259..a9f5c85
--- a/push2docker.sh
+++ b/push2docker.sh
@@ -1,4 +1,5 @@
 #!/bin/bash
 
-docker build -t my-shiny-app .
-docker push konradkraemer/biostats:latest
\ No newline at end of file
+docker build -t konradkraemer/biostats:latest .
+docker push konradkraemer/biostats:latest
+
diff --git a/run.sh b/run.sh
old mode 100644
new mode 100755
index e217024..18615e9
--- a/run.sh
+++ b/run.sh
@@ -3,5 +3,6 @@
 #/usr/bin/shiny-server
 sudo -u shiny /usr/bin/shiny-server
 
-# rstudio switch to terminal alt, shift, m
-# rstudio run command from script in terminal: strg, alt, enter
\ No newline at end of file
+#cd /srv/shiny-server
+
+#Rscript -e 'shiny::runApp(".", port = 3838)'
\ No newline at end of file
diff --git a/shinychem.Rproj b/shinychem.Rproj
deleted file mode 100644
index 8e3c2eb..0000000
--- a/shinychem.Rproj
+++ /dev/null
@@ -1,13 +0,0 @@
-Version: 1.0
-
-RestoreWorkspace: Default
-SaveWorkspace: Default
-AlwaysSaveHistory: Default
-
-EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
-Encoding: UTF-8
-
-RnwWeave: Sweave
-LaTeX: pdfLaTeX