Merge pull request #50 from aberHRML/devel

v2.5.1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: binneR
 Title: Spectral Processing for High Resolution Flow Infusion Mass Spectrometry
-Version: 2.5.0
+Version: 2.5.1
 Authors@R: person("Jasen", "Finch", email = "[email protected]", role = c("aut", "cre"))
 Description: A spectral binning approach for high resolution flow infusion mass spectrometry data.
 biocViews: MassSpectrometry, Metabolomics

NEWS.md

@@ -1,3 +1,9 @@
+# binneR v2.5.1
+
+* Performance and memory usage gains through ensuring 0 values are not read from raw files.
+
+* Added console output for processing steps to [`binneR::binneRlyse()`](https://aberhrml.github.io/binneR/reference/binneRlyse.html) and [`binneR::singleSample()](https://aberhrml.github.io/binneR/reference/singleSample.html).
+
 # binneR v2.5.0
 
 * S4 class [`Binalysis`](https://aberhrml.github.io/binneR/reference/Binalysis-class.html) now inherits from S4 class [`BinParameters`](https://aberhrml.github.io/binneR/reference/BinParameters-class.html).

R/allClasses.R

@@ -93,4 +93,4 @@ setValidity('Binalysis',function(object){
 	}
 
 
-})
+})

R/allGenerics.R

@@ -1,8 +1,8 @@
 
-setGeneric("spectralBinning", function(x)
+setGeneric("spectralBinning", function(x,verbose = TRUE)
 	standardGeneric("spectralBinning"))
 
-setGeneric("ss", function(x)
+setGeneric("ss", function(x, verbose = TRUE)
 	standardGeneric("ss"))
 
 #' @rdname results
@@ -87,3 +87,6 @@ setGeneric('plotPurity',function(x,histBins = 30)
 #' @rdname plotCentrality
 setGeneric('plotCentrality',function(x,histBins = 30)
 	standardGeneric('plotCentrality'))
+
+setGeneric('nScans',function(x)
+	standardGeneric('nScans'))

R/binneRlyse.R

@@ -21,7 +21,7 @@
 #' parameters <- detectParameters(files)
 #' cls(parameters) <- 'class'
 #' 
-#' #' ## Optionally declare parallel processing backend
+#' ## Optionally declare parallel processing backend
 #' # plan(future::multisession,workers = 2)
 #' 
 #' analysis <- binneRlyse(files, 
@@ -37,23 +37,23 @@
 #' @export
 
 binneRlyse <- function(files, 
-											 info, 
-											 parameters = binParameters(), 
-											 verbose = TRUE){
+																							info, 
+																							parameters = binParameters(), 
+																							verbose = TRUE){
 
-	analysis <- new('Binalysis',
-									parameters,
-									file_paths = files,
-									sample_info = info)
+	x <- new('Binalysis',
+										parameters,
+										creation_date = date(),
+										file_paths = files,
+										sample_info = info)
 
 	if (verbose == TRUE) {
 		startTime <- proc.time()
-		message(str_c('\n',
-									blue('binneR'),
-									red(str_c('v',
-														version(analysis))),
-									creationDate(analysis),
-									sep = ' '))		
+		message(str_c(blue('binneR'),
+																red(str_c('v',
+																										version(x))),
+																creationDate(x),
+																sep = ' '))		
 		message(str_c(str_c(rep('_',console_width()),collapse = ''),sep = ''))
 		params <- parameters %>%
 			{capture.output(print(.))} %>%
@@ -63,10 +63,11 @@ binneRlyse <- function(files,
 		message(str_c(str_c(rep('_',console_width()),collapse = ''),'\n',sep = ''))
 	}
 
-	analysis <- analysis %>% 
-		spectralBinning()
+	x <- x %>% 
+		spectralBinning(verbose = verbose)
 
 	if (verbose == TRUE) {
+		message()
 		endTime <- proc.time()
 		ellapsed <- {endTime - startTime} %>%
 			.[3] %>%
@@ -76,5 +77,5 @@ binneRlyse <- function(files,
 		message(str_c(green('Completed! '),ellapsed,sep = ''))
 	}
 
-	return(analysis)
+	return(x)
 }

R/calc.R

@@ -1,24 +1,34 @@
 
 calcBinList <- function(pks){
-        bins <- pks %>%
-                group_by(fileName,polarity,scan,bin) %>%
-                summarise(intensity = sum(intensity)) %>%
-                group_by(polarity,bin) %>%
-                summarise(count = n()) %>%
-                filter(count > 1) %>%
-                select(-count)
+  bins <- pks %>%
+    group_by(fileName,polarity,scan,bin) %>%
+    summarise(intensity = sum(intensity),
+              .groups = 'drop') %>%
+    group_by(polarity,bin) %>%
+    summarise(count = n(),
+              .groups = 'drop') %>%
+    filter(count > 1) %>%
+    select(-count)
 }
 
 calcBinMeasures <- function(pks,cls){
-        
-        binMeasures <- pks %>%
-                group_by_at(vars(all_of(c('fileName',
-                                          cls,
-                                          'polarity',
-                                          'bin')))) %>%
-                summarise(purity = binPurity(mz,intensity),
-                          centrality = binCentrality(mz,intensity),
-                          .groups = 'drop')
-        
-        return(binMeasures)
+
+  binMeasures <- pks %>%
+    group_by_at(vars(all_of(c('fileName',
+                              cls,
+                              'polarity',
+                              'bin')))) %>%
+    summarise(purity = binPurity(mz,intensity),
+              centrality = binCentrality(mz,intensity),
+              .groups = 'drop')
+
+  return(binMeasures)
 }
+
+setMethod('nScans',signature = 'Binalysis',
+          function(x){
+            x %>%
+              scans() %>%
+              unique() %>%
+              length()
+          })

R/get.R

@@ -39,7 +39,8 @@ getFile <- function(file,scans){
             d <- .
             d %>%
                 set_colnames(c('mz','intensity')) %>%
-                as_tibble()
+                as_tibble() %>%
+                filter(intensity > 0)
         }) %>%
         set_names(hd$seqNum) %>%
         bind_rows(.id = 'seqNum') %>%

R/singleSample.R

@@ -12,17 +12,17 @@
 #' @examples 
 #' file_path <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1]
 #' 
-#' #' ## Optionally declare parallel processing backend
+#' ## Optionally declare parallel processing backend
 #' # plan(future::multisession,workers = 2)
 #' 
 #' bd <- singleSample(file_path)
 #' @importFrom utils capture.output
 #' @export
 
 singleSample <- function(file, 
-												 class = NA, 
-												 verbose = TRUE){
-
+																									class = NA, 
+																									verbose = TRUE){
+	
 	if (length(file) > 1) {
 		stop('Only suitable for a single file!')	
 	}
@@ -35,25 +35,26 @@ singleSample <- function(file,
 	parameters <- detectParameters(file)
 
 	i <- tibble(fileOrder = seq_len(length(scans(parameters))),
-							fileName = basename(file),
-							injOrder = seq_len(length(scans(parameters))),
-							name = str_c('Scan ',scans(parameters)),
-							class = class,
-							batch = 1,
-							block = 1)
+													fileName = basename(file),
+													injOrder = seq_len(length(scans(parameters))),
+													name = str_c('Scan ',scans(parameters)),
+													class = class,
+													batch = 1,
+													block = 1)
 
 	x <-  new('Binalysis',
-						parameters,
-						file_paths = file,
-						sample_info = i)
+											parameters,
+											creation_date = date(),
+											file_paths = file,
+											sample_info = i)
 
 	if (!is.na(class)) {
 		cls(x) <- class	
 	}
 
 	if (verbose == TRUE) {
 		startTime <- proc.time()
-		message(str_c('\n',blue('binneR'),red(str_c('v',version(x))),creationDate(x),sep = ' '))		
+		message(str_c(blue('binneR'),red(str_c('v',version(x))),creationDate(x),sep = ' '))		
 		message(str_c(str_c(rep('_',console_width()),collapse = ''),sep = ''))
 		params <- parameters %>%
 			{capture.output(print(.))} %>%
@@ -64,9 +65,10 @@ singleSample <- function(file,
 	}
 
 	x <- x %>%
-		ss()
+		ss(verbose = verbose)
 
 	if (verbose == TRUE) {
+		message()
 		endTime <- proc.time()
 		ellapsed <- {endTime - startTime} %>%
 			.[3] %>%