add fractional and total ID rate modules to DART tab

modules/070_DART-ID/dart_04_fractional_ID_rate.R

@@ -0,0 +1,89 @@
+init <- function() {
+
+  type <- 'plot'
+  box_title <- 'Fractional ID Rate'
+  help_text <- 'Fractional rate of confident PSMs and PSMs from all MS2 scan events'
+  source_file <- 'evidence, msmsScans'
+
+  .validate <- function(data, input) {
+    validate(need(data()[['evidence']], paste0('Upload evidence.txt')))
+    validate(need(data()[['msmsScans']], paste0('Upload msmsScans.txt')))
+
+    # ensure that table has the DART-ID residual RT
+    validate(need(
+      'dart_PEP' %in% colnames(data()[['evidence']]), 
+      paste0('Provide evidence.txt from DART-ID output, with updated dart_PEP column')
+    ))
+  }
+
+  .plotdata <- function(data, input) {
+
+    # MS2 Scans and PSMs
+    a <- data()[['msmsScans']] %>%
+      dplyr::select('Raw.file', 'Sequence') %>%
+      dplyr::group_by(Raw.file) %>%
+      dplyr::summarise(scans=dplyr::n(),
+                       psms=sum(as.character(Sequence) != ' ', na.rm=T)) %>%
+      dplyr::arrange(Raw.file)
+
+    # IDs at 1e-2 PEP, 1e-2 DART PEP
+    b <- data()[['evidence']] %>%
+      dplyr::select('Raw.file', 'Sequence', 'PEP', 'dart_PEP') %>%
+      dplyr::group_by(Raw.file) %>%
+      dplyr::summarise(ids=sum(PEP < 0.01, na.rm=T),
+                       dart_ids=sum(dart_PEP < 0.01, na.rm=T)) %>%
+      dplyr::arrange(Raw.file)
+    if(nrow(a) == nrow(b)){
+      plotdata <- cbind(a, b[,-1]) %>%
+        # get fractional rates, i.e., fraction of MSMS scans
+        dplyr::mutate(psms = psms / scans,
+                      ids = ids / scans,
+                      dart_ids = dart_ids / scans) %>%
+        # gather = dplyr equiv. of reshape2::melt
+        tidyr::gather(key, value, -Raw.file) %>%
+        # remove msms scans
+        dplyr::filter(key != 'scans') %>%
+        # rename levels
+        dplyr::mutate(key=factor(key, labels=c('IDs @ DART PEP < 0.01', 'IDs @ PEP < 0.01', 'PSMs')))
+    }else if((nrow(a) > 0) & (nrow(b) == 0)){
+      plotdata <- a %>%
+        tidyr::gather(key, value, -Raw.file) %>%
+        # rename levels
+        dplyr::mutate(key=factor(key, labels=c('PSMs')))
+    }else if((nrow(a) == 0) & (nrow(b) > 0)){
+      plotdata <- b %>% 
+        tidyr::gather(key, value, -Raw.file) %>%
+        # rename levels
+        dplyr::mutate(key=factor(key, labels=c('IDs @ DART PEP < 0.01', 'IDs @ PEP < 0.01', 'PSMs')))
+    }
+    return(plotdata)
+  }
+
+  .plot <- function(data, input) {
+    .validate(data, input)
+    plotdata <- .plotdata(data, input)
+
+    validate(need((nrow(plotdata) > 1), paste0('No Rows selected')))
+
+    ggplot(plotdata, aes(Raw.file, value, fill=key)) +
+      geom_bar(stat='identity', position='dodge') +
+      labs(x='Experiment', y='Fraction', fill='Category') +
+      theme_base(input=input, show_legend=T) +
+      # keep the legend
+      theme(legend.position='right',
+            legend.key=element_rect(fill='white'))
+  }
+
+  return(list(
+    type=type,
+    box_title=box_title,
+    help_text=help_text,
+    source_file=source_file,
+    validate_func=.validate,
+    plotdata_func=.plotdata,
+    plot_func=.plot,
+    dynamic_width=150,
+    dynamic_width_base=300
+  ))
+}
+

modules/070_DART-ID/dart_05_total_ID_rate.R

@@ -0,0 +1,83 @@
+init <- function() {
+
+  type <- 'plot'
+  box_title <- 'Total ID Rate'
+  help_text <- 'Number of MSMS scans, PSMs, and confident PSMs'
+  source_file <- 'evidence, msmsScans'
+
+  .validate <- function(data, input) {
+    validate(need(data()[['evidence']], paste0('Upload evidence.txt')))
+    validate(need(data()[['msmsScans']], paste0('Upload msmsScans.txt')))
+
+    # ensure that table has the DART-ID residual RT
+    validate(need(
+      'dart_PEP' %in% colnames(data()[['evidence']]), 
+      paste0('Provide evidence.txt from DART-ID output, with updated dart_PEP column')
+    ))
+  }
+
+  .plotdata <- function(data, input) {
+
+    # MS2 Scans and PSMs
+    a <- data()[['msmsScans']] %>%
+      dplyr::select('Raw.file', 'Sequence') %>%
+      dplyr::group_by(Raw.file) %>%
+      dplyr::summarise(scans=dplyr::n(),
+                       psms=sum(as.character(Sequence) != ' ', na.rm=T)) %>%
+      dplyr::arrange(Raw.file)
+
+    # IDs at 5e-2 and 1e-2 PEP
+    b <- data()[['evidence']] %>%
+      dplyr::select('Raw.file', 'Sequence', 'PEP', 'dart_PEP') %>%
+      dplyr::group_by(Raw.file) %>%
+      dplyr::summarise(ids=sum(PEP < 0.01, na.rm=T),
+                       dart_ids=sum(dart_PEP < 0.01, na.rm=T)) %>%
+      dplyr::arrange(Raw.file)
+    if(nrow(a) == nrow(b)){
+      plotdata <- cbind(a, b[,-1]) %>%
+        # gather = dplyr equiv. of reshape2::melt
+        tidyr::gather(key, value, -Raw.file) %>%
+        # rename levels
+        dplyr::mutate(key=factor(key, labels=c('IDs @ DART PEP < 0.01', 'IDs @ PEP < 0.01', 'PSMs', 'MSMSs')))
+    }else if((nrow(a) > 0) & (nrow(b) == 0)){
+      plotdata <- a %>%
+        tidyr::gather(key, value, -Raw.file) %>%
+        # rename levels
+        dplyr::mutate(key=factor(key, labels=c('PSMs', 'MSMSs')))
+    }else if((nrow(a) == 0) & (nrow(b) > 0)){
+      plotdata <- b %>%
+        tidyr::gather(key, value, -Raw.file) %>%
+        # rename levels
+        dplyr::mutate(key=factor(key, labels=c('IDs @ DART PEP < 0.01', 'IDs @ PEP < 0.01')))
+    }
+    return(plotdata)
+  }
+
+  .plot <- function(data, input) {
+    .validate(data, input)
+    plotdata <- .plotdata(data, input)
+
+    validate(need((nrow(plotdata) > 1), paste0('No Rows selected')))
+
+    ggplot(plotdata, aes(Raw.file, value, fill=key)) +
+      geom_bar(stat='identity', position='dodge') +
+      labs(x='Experiment', y='Fraction', fill='Category') +
+      theme_base(input=input, show_legend=T) +
+      # keep the legend
+      theme(legend.position='right',
+            legend.key=element_rect(fill='white'))
+  }
+
+  return(list(
+    type=type,
+    box_title=box_title,
+    help_text=help_text,
+    source_file=source_file,
+    validate_func=.validate,
+    plotdata_func=.plotdata,
+    plot_func=.plot,
+    dynamic_width=150,
+    dynamic_width_base=300
+  ))
+}
+