From 6454193ce0875874d3fe2b9e7144fa7c80207428 Mon Sep 17 00:00:00 2001
From: GeorgWa <gewaelbe@googlemail.com>
Date: Wed, 19 Apr 2023 10:50:33 +0200
Subject: [PATCH 1/4] updated data availability

---
 docs/index.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/docs/index.md b/docs/index.md
index d2f82e2..2d909c1 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -87,6 +87,9 @@ DO-MS is distributed by an [MIT license]({{site.github_link}}/blob/master/LICENS
 
 Please feel free to contribute to this project by opening an issue or pull request in the [GitHub repository]({{site.github_link}}).
 
+### Data Availability
+DO-MS reports and example data can be found [Here]({{site.baseurl}}/docs/DO-MS_examples). All Raw Data and search engine results from the DO-MS DIA paper are avilable on MassIVE under the following id: MSV000091733.
+
 -------------
 
 ## Help!

From 5ffde4740bd80f7cf170e3bad7974ae85545dca3 Mon Sep 17 00:00:00 2001
From: GeorgWa <gewaelbe@googlemail.com>
Date: Wed, 19 Apr 2023 10:51:26 +0200
Subject: [PATCH 2/4] typo

---
 docs/index.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/index.md b/docs/index.md
index 2d909c1..5104664 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -88,7 +88,7 @@ DO-MS is distributed by an [MIT license]({{site.github_link}}/blob/master/LICENS
 Please feel free to contribute to this project by opening an issue or pull request in the [GitHub repository]({{site.github_link}}).
 
 ### Data Availability
-DO-MS reports and example data can be found [Here]({{site.baseurl}}/docs/DO-MS_examples). All Raw Data and search engine results from the DO-MS DIA paper are avilable on MassIVE under the following id: MSV000091733.
+DO-MS reports and example data can be found [Here]({{site.baseurl}}/docs/DO-MS_examples). All raw data and search engine results from the DO-MS DIA paper are avilable on MassIVE under the following id: MSV000091733.
 
 -------------
 

From 2b833af62b69d94f86dabd0427ae5c6b2f9936c8 Mon Sep 17 00:00:00 2001
From: GeorgWa <gewaelbe@googlemail.com>
Date: Sun, 30 Jul 2023 18:16:44 +0200
Subject: [PATCH 3/4] fix -inf PEP

---
 server/generate_report.R | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/server/generate_report.R b/server/generate_report.R
index 0f6a9cc..a8c4276 100644
--- a/server/generate_report.R
+++ b/server/generate_report.R
@@ -34,13 +34,19 @@ generate_report <- function(input, filtered_data, exp_sets, file, progress_bar=F
     progress$inc(5/100, detail='Initializing')
   }
   
-  pep_max<-signif(max(filtered_data()[['evidence']][,"PEP"]),2)  
+  pep_max<-signif(max(filtered_data()[['evidence']][,"PEP"]),2)
+  
+  pep_info = ''
+  
+  if ((pep_max <= 1) && (pep_max >= 0)) {
+    pep_info = paste0(" | PEP < ",pep_max)
+  }
   
   report <- paste(
     '---',
     paste0('title: DO-MS Report'
     ),
-    paste0('date: "`r paste0(\'Version: ', version, " | PEP < ",pep_max, ' | \',  format(Sys.time(), \'Generated: %Y-%m-%d    %H:%M:%S\'))`"'),
+    paste0('date: "`r paste0(\'Version: ', version, pep_info, ' | \',  format(Sys.time(), \'Generated: %Y-%m-%d    %H:%M:%S\'))`"'),
     'output:',
 #    paste0('data filtered to PEP < ',
 #           pep_max),

From 547a17412e682b72c292095847733883de8cc4ef Mon Sep 17 00:00:00 2001
From: GeorgWa <gewaelbe@googlemail.com>
Date: Sun, 30 Jul 2023 18:24:30 +0200
Subject: [PATCH 4/4] updated module descriptions

---
 global.R                                                    | 2 +-
 .../020_Ion_Sampling/Instrument_08_ms1_fill_time_dist.R     | 4 ++--
 .../dia-nn/020_Ion_Sampling/Instrument_09_ms1_fill_times.R  | 4 ++--
 modules/dia-nn/020_Ion_Sampling/Instrument_10_ms1_tic.R     | 4 ++--
 .../020_Ion_Sampling/Instrument_11_ms2_fill_time_dist.R     | 4 ++--
 .../dia-nn/020_Ion_Sampling/Instrument_12_ms2_fill_times.R  | 4 ++--
 .../020_Ion_Sampling/Instrument_13_ms2_fill_time_matrix.R   | 4 ++--
 .../020_Ion_Sampling/instrument_01_DIA_MS1_int_ID_Label.R   | 2 +-
 modules/dia-nn/020_Ion_Sampling/instrument_02_IDs_by_RT.R   | 2 +-
 .../instrument_05_DIA_MS1_Intersected_int_Norm.R            | 2 +-
 .../dia-nn/020_Ion_Sampling/instrument_06_charge_count.R    | 2 +-
 .../dia-nn/020_Ion_Sampling/instrument_14_DIA_MS1_counts.R  | 6 ++----
 .../030_Identifications/00_PEP_colored_cumulative_update.R  | 2 +-
 modules/dia-nn/030_Identifications/01_ms1vsms2_IDs.R        | 2 +-
 modules/dia-nn/030_Identifications/02_modified_IDs.R        | 2 +-
 modules/dia-nn/030_Identifications/05_miscleavage_table.R   | 2 +-
 16 files changed, 23 insertions(+), 25 deletions(-)

diff --git a/global.R b/global.R
index a5f0851..e494db2 100644
--- a/global.R
+++ b/global.R
@@ -1,4 +1,4 @@
-version <- '2.0.5'
+version <- '2.0.6'
 
 # check R version. required R >= 3.5.0 & R <= 4.0.2
 if(as.numeric(R.Version()$major) < 4) {
diff --git a/modules/dia-nn/020_Ion_Sampling/Instrument_08_ms1_fill_time_dist.R b/modules/dia-nn/020_Ion_Sampling/Instrument_08_ms1_fill_time_dist.R
index 9699b6c..73e7b45 100644
--- a/modules/dia-nn/020_Ion_Sampling/Instrument_08_ms1_fill_time_dist.R
+++ b/modules/dia-nn/020_Ion_Sampling/Instrument_08_ms1_fill_time_dist.R
@@ -1,8 +1,8 @@
 init <- function() {
   
   type <- 'plot'
-  box_title <- 'Ms1 Fill Time Distribution'
-  help_text <- 'Ms1 fill times along gradient'
+  box_title <- 'MS1 Fill Time Distribution'
+  help_text <- 'Histogram showing the distribution of all MS1 fill times.'
   source_file <- 'report'
   
   .validate <- function(data, input) {
diff --git a/modules/dia-nn/020_Ion_Sampling/Instrument_09_ms1_fill_times.R b/modules/dia-nn/020_Ion_Sampling/Instrument_09_ms1_fill_times.R
index 5bcc63d..8065672 100644
--- a/modules/dia-nn/020_Ion_Sampling/Instrument_09_ms1_fill_times.R
+++ b/modules/dia-nn/020_Ion_Sampling/Instrument_09_ms1_fill_times.R
@@ -1,8 +1,8 @@
 init <- function() {
   
   type <- 'plot'
-  box_title <- 'Ms1 Fill Times along Gradient'
-  help_text <- 'The averge fill time is shown in magenta for different bins along the retention time gradient. The standard deviation is depicted as area in blue, scans outside this area are shown as single datapoints.'
+  box_title <- 'MS1 Fill Times along Gradient'
+  help_text <- 'The average fill time is shown in magenta for different bins along the retention time gradient. The standard deviation is depicted as an area in blue, and scans outside this area are shown as single data points.'
   source_file <- 'report'
   
   .validate <- function(data, input) {
diff --git a/modules/dia-nn/020_Ion_Sampling/Instrument_10_ms1_tic.R b/modules/dia-nn/020_Ion_Sampling/Instrument_10_ms1_tic.R
index fc94c2f..d5a8829 100644
--- a/modules/dia-nn/020_Ion_Sampling/Instrument_10_ms1_tic.R
+++ b/modules/dia-nn/020_Ion_Sampling/Instrument_10_ms1_tic.R
@@ -1,8 +1,8 @@
 init <- function() {
   
   type <- 'plot'
-  box_title <- 'Ms1 total Ion Current along Gradient'
-  help_text <- 'The toal Ion Current (TIC) is shown for bins along the retention time gradient.'
+  box_title <- 'MS1 TIC along Gradient'
+  help_text <- 'The total Ion Current (TIC) is shown for bins along the retention time gradient.'
   source_file <- 'report'
   
   .validate <- function(data, input) {
diff --git a/modules/dia-nn/020_Ion_Sampling/Instrument_11_ms2_fill_time_dist.R b/modules/dia-nn/020_Ion_Sampling/Instrument_11_ms2_fill_time_dist.R
index 490114b..b5c109f 100644
--- a/modules/dia-nn/020_Ion_Sampling/Instrument_11_ms2_fill_time_dist.R
+++ b/modules/dia-nn/020_Ion_Sampling/Instrument_11_ms2_fill_time_dist.R
@@ -1,8 +1,8 @@
 init <- function() {
   
   type <- 'plot'
-  box_title <- 'Ms2 Fill Time Distribution'
-  help_text <- 'Ms2 fill times along gradient'
+  box_title <- 'MS2 Fill Time Distribution'
+  help_text <- 'Histogram showing the distribution of all MS2 fill times.'
   source_file <- 'report'
   
   .validate <- function(data, input) {
diff --git a/modules/dia-nn/020_Ion_Sampling/Instrument_12_ms2_fill_times.R b/modules/dia-nn/020_Ion_Sampling/Instrument_12_ms2_fill_times.R
index 2ea6b37..b478277 100644
--- a/modules/dia-nn/020_Ion_Sampling/Instrument_12_ms2_fill_times.R
+++ b/modules/dia-nn/020_Ion_Sampling/Instrument_12_ms2_fill_times.R
@@ -1,8 +1,8 @@
 init <- function() {
   
   type <- 'plot'
-  box_title <- 'Ms2 Fill Times along Gradient'
-  help_text <- 'The averge fill time is shown in magenta for different bins along the retention time gradient. The standard deviation is depicted as area in blue, scans outside this area are shown as single datapoints.'
+  box_title <- 'MS2 Fill Times along Gradient'
+  help_text <- 'The average fill time is shown in magenta for different bins along the retention time gradient. The standard deviation is depicted as an area in blue, and scans outside this area are shown as single data points.'
   source_file <- 'report'
   
   .validate <- function(data, input) {
diff --git a/modules/dia-nn/020_Ion_Sampling/Instrument_13_ms2_fill_time_matrix.R b/modules/dia-nn/020_Ion_Sampling/Instrument_13_ms2_fill_time_matrix.R
index 38bd750..4f2db86 100644
--- a/modules/dia-nn/020_Ion_Sampling/Instrument_13_ms2_fill_time_matrix.R
+++ b/modules/dia-nn/020_Ion_Sampling/Instrument_13_ms2_fill_time_matrix.R
@@ -1,8 +1,8 @@
 init <- function() {
   
   type <- 'plot'
-  box_title <- 'Ms2 Fill Time Matrix'
-  help_text <- 'The average Ms2 fill times are shown across the gradient for every distinct Ms2 window.'
+  box_title <- 'MS2 Fill Time Matrix'
+  help_text <- 'The average MS2 fill times are shown across the gradient for every distinct MS2 window.'
   source_file <- 'fill_times'
   
   .validate <- function(data, input) {
diff --git a/modules/dia-nn/020_Ion_Sampling/instrument_01_DIA_MS1_int_ID_Label.R b/modules/dia-nn/020_Ion_Sampling/instrument_01_DIA_MS1_int_ID_Label.R
index a6a5ccd..f44ecbf 100644
--- a/modules/dia-nn/020_Ion_Sampling/instrument_01_DIA_MS1_int_ID_Label.R
+++ b/modules/dia-nn/020_Ion_Sampling/instrument_01_DIA_MS1_int_ID_Label.R
@@ -2,7 +2,7 @@ init <- function() {
   
   type <- 'plot'
   box_title <- 'Channel wise MS1 Intensity for Precursors'
-  help_text <- 'Plotting the MS1 intensity for all precursors which were associated with one of the defined channels.'
+  help_text <- 'Plotting the MS1 intensity for all precursors associated with one of the defined channels.'
   source_file <- 'report'
   
   .validate <- function(data, input) {
diff --git a/modules/dia-nn/020_Ion_Sampling/instrument_02_IDs_by_RT.R b/modules/dia-nn/020_Ion_Sampling/instrument_02_IDs_by_RT.R
index 4e1e82c..2b71269 100644
--- a/modules/dia-nn/020_Ion_Sampling/instrument_02_IDs_by_RT.R
+++ b/modules/dia-nn/020_Ion_Sampling/instrument_02_IDs_by_RT.R
@@ -2,7 +2,7 @@ init <- function() {
   
   type <- 'plot'
   box_title <- 'Precursors Identified across Gradient'
-  help_text <- 'Precursor are plotted across the chromatographic gradient.'
+  help_text <- 'Plotting the precursors across the chromatographic gradient.'
   source_file <- 'report'
   
   .validate <- function(data, input) {
diff --git a/modules/dia-nn/020_Ion_Sampling/instrument_05_DIA_MS1_Intersected_int_Norm.R b/modules/dia-nn/020_Ion_Sampling/instrument_05_DIA_MS1_Intersected_int_Norm.R
index 7abacf9..6e8916d 100644
--- a/modules/dia-nn/020_Ion_Sampling/instrument_05_DIA_MS1_Intersected_int_Norm.R
+++ b/modules/dia-nn/020_Ion_Sampling/instrument_05_DIA_MS1_Intersected_int_Norm.R
@@ -2,7 +2,7 @@ init <- function() {
   
   type <- 'plot'
   box_title <- 'Normalized MS1 Intensity for Intersected Precursors'
-  help_text <- 'Plotting the MS1 Intensity for intersected precursors summed over all channels. Experiments are normalized to the first experiment. '
+  help_text <- 'Plotting the MS1 intensity for intersected precursors summed over all channels. Experiments are normalized to the first experiment.'
   source_file <- 'report'
   
   .validate <- function(data, input) {
diff --git a/modules/dia-nn/020_Ion_Sampling/instrument_06_charge_count.R b/modules/dia-nn/020_Ion_Sampling/instrument_06_charge_count.R
index 8ecb113..7104580 100644
--- a/modules/dia-nn/020_Ion_Sampling/instrument_06_charge_count.R
+++ b/modules/dia-nn/020_Ion_Sampling/instrument_06_charge_count.R
@@ -2,7 +2,7 @@ init <- function() {
 
   type <- 'plot'
   box_title <- 'Number of Precursors by Charge State'
-  help_text <- 'Number of precursors observed during MS1 scans by charge state'
+  help_text <- 'Number of precursors observed during MS1 scans by charge state.'
   source_file <- 'report'
 
   
diff --git a/modules/dia-nn/020_Ion_Sampling/instrument_14_DIA_MS1_counts.R b/modules/dia-nn/020_Ion_Sampling/instrument_14_DIA_MS1_counts.R
index 636893b..e35d253 100644
--- a/modules/dia-nn/020_Ion_Sampling/instrument_14_DIA_MS1_counts.R
+++ b/modules/dia-nn/020_Ion_Sampling/instrument_14_DIA_MS1_counts.R
@@ -1,10 +1,8 @@
 init <- function() {
   
   type <- 'plot'
-  box_title <- 'Channel wise MS1 Copy Number for Precursors'
-  help_text <- 'Plotting the MS1 copy numbers for all precursors which were associated with one of the defined channels. 
-  The copy numbers are calculated using the signal to noise ratio as described in Derks et al. 2022. By default a resolution of 70,000 is used during preprocessing. It can be changed with the --resolution parameter'
-  source_file <- 'sn'
+  box_title <- 'Channel-wise MS1 Copy Number for Precursors'
+  help_text <- 'Plotting the MS1 copy numbers for all precursors associated with one of the defined channels. The copy numbers are calculated using the signal-to-noise ratio as described in Derks et al. 2022. By default, a resolution of 70,000 is used during preprocessing. It can be changed with the –resolution parameter.'
   
   .validate <- function(data, input) {
     validate(need(data()[['sn']], paste0('Upload report.txt')))
diff --git a/modules/dia-nn/030_Identifications/00_PEP_colored_cumulative_update.R b/modules/dia-nn/030_Identifications/00_PEP_colored_cumulative_update.R
index dc2b730..2bb71eb 100644
--- a/modules/dia-nn/030_Identifications/00_PEP_colored_cumulative_update.R
+++ b/modules/dia-nn/030_Identifications/00_PEP_colored_cumulative_update.R
@@ -2,7 +2,7 @@ init <- function() {
   
   type <- 'plot'
   box_title <- 'Number of Confident Precursor Identifications'
-  help_text <- 'Plotting the number of precursors identified at each given confidence level.'
+  help_text <- 'Plotting the number of precursors identified as a function of the false discovery rate (FDR).'
   source_file <- 'report'
 
   .validate <- function(data, input) {
diff --git a/modules/dia-nn/030_Identifications/01_ms1vsms2_IDs.R b/modules/dia-nn/030_Identifications/01_ms1vsms2_IDs.R
index 5d75910..018c7b6 100644
--- a/modules/dia-nn/030_Identifications/01_ms1vsms2_IDs.R
+++ b/modules/dia-nn/030_Identifications/01_ms1vsms2_IDs.R
@@ -2,7 +2,7 @@ init <- function() {
   
   type <- 'plot'
   box_title <-  'Precursors by Quantification Strategy'
-  help_text <- 'Number of precursors found based on quantification startegy. Ms2 precursors are counted based on Precursor.Quantity > 0 and Ms1 precursors are counted based on Ms1.Area > 0.'
+  help_text <- 'Number of precursors found based on quantification startegy. MS2 precursors are counted based on Precursor.Quantity > 0 and MS1 precursors are counted based on Ms1.Area > 0.'
   source_file <- 'report'
   
   .validate <- function(data, input) {
diff --git a/modules/dia-nn/030_Identifications/02_modified_IDs.R b/modules/dia-nn/030_Identifications/02_modified_IDs.R
index 13a777c..dd43928 100644
--- a/modules/dia-nn/030_Identifications/02_modified_IDs.R
+++ b/modules/dia-nn/030_Identifications/02_modified_IDs.R
@@ -2,7 +2,7 @@ init <- function() {
   
   type <- 'plot'
   box_title <-  'Precursors by Modification'
-  help_text <- 'Number of precursors found based on modification types specified'
+  help_text <- 'Number of precursors found based on modification types specified.'
   source_file <- 'report'
   
   .validate <- function(data, input) {
diff --git a/modules/dia-nn/030_Identifications/05_miscleavage_table.R b/modules/dia-nn/030_Identifications/05_miscleavage_table.R
index e419c86..361c44d 100644
--- a/modules/dia-nn/030_Identifications/05_miscleavage_table.R
+++ b/modules/dia-nn/030_Identifications/05_miscleavage_table.R
@@ -2,7 +2,7 @@ init <- function() {
   
   type <- 'table'
   box_title <- 'Miscleavage Rate (percentage), PEP < 0.01'
-  help_text <- 'Miscleavage rate (percentage) for precursors identified with confidence PEP < 0.01'
+  help_text <- 'Miscleavage rate (percentage) for precursors identified with confidence PEP < 0.01.'
   source_file <- 'report'
   
   .validate <- function(data, input) {