From a4d305d44bf2a49462d1eb8c957bb992deecc0ca Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Mon, 2 Nov 2020 16:36:52 +0000
Subject: [PATCH] added TASK at the beginning of the scripts

---
 boxplot_stat_all.R      | 10 ++++++++++
 boxplot_stat_function.R | 17 ++++++++++++++++-
 boxplot_stat_log.R      | 12 +++++++++++-
 3 files changed, 37 insertions(+), 2 deletions(-)

diff --git a/boxplot_stat_all.R b/boxplot_stat_all.R
index 74cf819..ac29943 100755
--- a/boxplot_stat_all.R
+++ b/boxplot_stat_all.R
@@ -3,6 +3,16 @@ getwd()
 setwd("~/git/mosaic_2020/")
 getwd()
 ###############################################################
+# TASK: boxplots with stats for NPA, SAM and SERUM 
+# for each mediator, at each timepoint by group
+
+# TODO: check boxplot_stat_function.R
+# output plots even if stats fail due to data containing only LLODs
+# however for a given mediator, if there is error for ANY timepoint
+# stats will not be added for the entire plot! To be handled in 
+# next iteration!
+###############################################################
+
 #=============
 # Input
 #=============
diff --git a/boxplot_stat_function.R b/boxplot_stat_function.R
index 0e02f3b..2ad5a07 100755
--- a/boxplot_stat_function.R
+++ b/boxplot_stat_function.R
@@ -3,7 +3,22 @@ getwd()
 setwd("~/git/mosaic_2020/")
 getwd()
 ############################################################
-# TASK: boxplots with stats
+# TASK: Boxplots with stats 
+# for each mediator, at each timepoint by group
+
+# Handles some error: i.e will continue plotting even if there
+# is stats error. However, needs fixing see below point 1):
+
+# FIXME: 
+# 1) For a given mediator, if there is error for ANY timepoint
+# stats will not be added for the entire plot!
+
+# 2) make the function more generic to take the following inputs
+# df, column, group
+# this way you can directly pass the log_calculated value column
+
+# To be handled in 
+# next iteration!
 ############################################################
 
 is.error <- function(x) inherits(x, "try-error")
diff --git a/boxplot_stat_log.R b/boxplot_stat_log.R
index 8a73597..e126a00 100755
--- a/boxplot_stat_log.R
+++ b/boxplot_stat_log.R
@@ -3,11 +3,21 @@ getwd()
 setwd("~/git/mosaic_2020/")
 getwd()
 ###############################################################
+# TASK: boxplots with stats for NPA, SAM and SERUM but with log scale
+# for each mediator, at each timepoint, by group
+
+# TODO: check boxplot_stat_function.R
+# output plots even if stats fail due to data containing only LLODs
+# however for a given mediator, if there is error for ANY timepoint
+# stats will not be added for the entire plot! To be handled in 
+# next iteration!
+###############################################################
+
 #=============
 # Input
 #=============
 source("boxplot_stat_function.R")
-source("boxplot_function.R")
+#source("boxplot_function.R") for sam
 source("plot_data.R")
 
 #=============