adapt to latest DART-ID version

SlavovLab · May 10, 2019 · 2603a5f · 2603a5f
1 parent ebb4cd0
commit 2603a5f
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Showing 3 changed files with 19 additions and 18 deletions.
diff --git a/modules/070_DART-ID/dart_00_pep_scatter.R b/modules/070_DART-ID/dart_00_pep_scatter.R
@@ -12,8 +12,8 @@ init <- function() {
 
     # ensure that table has the DART-ID PEP
     validate(need(
-      'pep_updated' %in% colnames(data()[['evidence']]), 
-      paste0('Provide evidence.txt from DART-ID output, with updated PEP column')
+      'dart_PEP' %in% colnames(data()[['evidence']]), 
+      paste0('Provide evidence.txt from DART-ID output, with updated dart_PEP column')
     ))
   }
 
@@ -22,12 +22,12 @@ init <- function() {
     conf_limit <- 1e-8
 
     ev.f <- data()[['evidence']] %>%
-      dplyr::select(c('Sequence', 'PEP', 'pep_new')) %>%
-      dplyr::filter(!is.na(pep_new)) %>%
-      dplyr::filter(PEP > 0 & pep_new > 0 & PEP > conf_limit & pep_new > conf_limit) %>%
-      dplyr::mutate_at(c('PEP', 'pep_new'), funs(ifelse(. > 1, 1, .))) %>%
+      dplyr::select(c('Sequence', 'PEP', 'dart_PEP')) %>%
+      dplyr::filter(!PEP == dart_PEP) %>%
+      dplyr::filter(PEP > 0 & dart_PEP > 0 & PEP > conf_limit & dart_PEP > conf_limit) %>%
+      dplyr::mutate_at(c('PEP', 'dart_PEP'), funs(ifelse(. > 1, 1, .))) %>%
       dplyr::mutate(pep_log=log10(PEP),
-                    pep_new_log=log10(pep_new))
+                    pep_new_log=log10(dart_PEP))
 
     return(ev.f)
   }
@@ -61,7 +61,7 @@ init <- function() {
     rng <- seq(-5, 0, 1)
     nbins <- 80
 
-    ggplot(plotdata, aes(x=PEP, y=pep_new)) +
+    ggplot(plotdata, aes(x=PEP, y=dart_PEP)) +
       stat_bin2d(bins=nbins, drop=TRUE, geom='tile', aes(fill=..density..)) +
       geom_abline(slope=1, intercept=0, color='black', size=0.5) +
       geom_vline(xintercept=1e-2, linetype='dotted', color='black', size=0.5) +

diff --git a/modules/070_DART-ID/dart_01_fdr_increase.R b/modules/070_DART-ID/dart_01_fdr_increase.R
@@ -11,21 +11,22 @@ init <- function() {
 
     # ensure that table has the DART-ID PEP
     validate(need(
-      'pep_updated' %in% colnames(data()[['evidence']]), 
-      paste0('Provide evidence.txt from DART-ID output, with updated PEP column')
+      'dart_PEP' %in% colnames(data()[['evidence']]), 
+      paste0('Provide evidence.txt from DART-ID output, with updated dart_PEP column')
     ))
   }
 
   .plotdata <- function(data, input) {
     ev <- data()[['evidence']] 
     ev <- ev %>%
+      filter(!is.na(PEP) & !is.na(dart_PEP)) %>%
       # ceil PEPs to 1
-      dplyr::mutate_at(c('PEP', 'pep_updated'), funs(ifelse(. > 1, 1, .))) %>%
+      dplyr::mutate_at(c('PEP', 'dart_PEP'), funs(ifelse(. > 1, 1, .))) %>%
       # calculate q-values
       dplyr::mutate(qval=(cumsum(PEP[order(PEP)]) /
                           seq(1, nrow(ev)))[order(order(PEP))],
-                    qval_updated=(cumsum(pep_updated[order(pep_updated)]) /
-                                  seq(1, nrow(ev)))[order(order(pep_updated))])
+                    qval_updated=(cumsum(dart_PEP[order(dart_PEP)]) /
+                                  seq(1, nrow(ev)))[order(order(dart_PEP))])
 
     # flag peptides that don't have a single confident ID across all sets
     new_peptides <- ev %>%

diff --git a/modules/070_DART-ID/dart_03_ids_per_exp.R b/modules/070_DART-ID/dart_03_ids_per_exp.R
@@ -11,8 +11,8 @@ init <- function() {
 
     # ensure that table has the DART-ID residual RT
     validate(need(
-      'pep_updated' %in% colnames(data()[['evidence']]), 
-      paste0('Provide evidence.txt from DART-ID output, with residual RT column \"residual\"')
+      'dart_PEP' %in% colnames(data()[['evidence']]), 
+      paste0('Provide evidence.txt from DART-ID output, with updated dart_PEP column.')
     ))
 
   }
@@ -21,12 +21,12 @@ init <- function() {
     ev <- data()[['evidence']]
 
     plotdata <- ev %>%
-      dplyr::select(c('Raw.file', 'Modified.sequence', 'PEP', 'pep_updated')) %>%
+      dplyr::select(c('Raw.file', 'Modified.sequence', 'PEP', 'dart_PEP')) %>%
       dplyr::group_by(Raw.file) %>%
       dplyr::summarise(
         file=unique(Raw.file),
-        ids=sum(PEP < 0.01),
-        new_ids=sum(pep_updated < 0.01))
+        ids=sum(PEP < 0.01, na.rm=T),
+        new_ids=sum(dart_PEP < 0.01, na.rm=T))
 
     return(plotdata)
   }