Commiting branch GCAT_6.0 at SVN revision 572

R/GCAT/DESCRIPTION

@@ -8,11 +8,10 @@ Description: Imports high-throughput growth curve data from microtiter
   GCAT estimates important growth characteristics
   (specific growth rate, maximum growth capacity, and lag time)
   for each well in a read.
-  The code was written by Jason Shao (no longer at GLBRC) and Nate DiPiazza.
-Version: 5.0.2
+Version: 6.0.1
 Depends: pheatmap, gplots, methods
 Maintainer: Yury Bukhman <ybukhman@glbrc.wisc.edu>
 License: LGPL-3
-Date: 2015-04-21
+Date: 2015-06-11
 Author: Jason Shao, Nate DiPiazza <ndipiazza@wisc.edu>, Minh Duc Bui, Yury V Bukhman
 Suggests: testthat

R/GCAT/GCAT.Rproj

@@ -14,4 +14,4 @@ LaTeX: pdfLaTeX
 
 BuildType: Package
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd
+PackageRoxygenize: rd,collate,namespace

R/GCAT/NAMESPACE

@@ -19,6 +19,7 @@ exportMethods(getStartIndex)
 exportMethods(getUseLog)
 exportMethods(getWellInfo)
 exportMethods(getnls)
+exportMethods(plot)
 import(gplots)
 import(methods)
 import(pheatmap)

R/GCAT/R/GCAT.main.R

@@ -90,7 +90,7 @@ global.version.number = packageDescription(pkg="GCAT")$Version
 #' @param use.loess Whether to use LOESS model or not?
 #' @param smooth.param Smoothing parameter for LOESS model.
 #' @param add.constant A numeric constant that will be added to each curve before the log transform (defaults to 1) 
-#' @param blank.value User can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well. 
+#' @param blank.value User can enter a blank OD measurement for uninoculated wells. if NULL, assumes the first OD measurement of each well to be blank. 
 #' @param start.index Which timepoint should be used as the first one after inoculation (defaults to the 2th one)
 #' @param growth.cutoff Minimum threshold for curve growth. 
 #' @param points.to.remove A list of numbers referring to troublesome points that should be removed across all wells.
@@ -115,7 +115,7 @@ global.version.number = packageDescription(pkg="GCAT")$Version
 #' @export
 gcat.analysis.main = function(file.list, single.plate, layout.file = NULL,   
   out.dir = getwd(), graphic.dir = paste(out.dir, "/pics", sep = ""), 
-  add.constant = 0, blank.value = NULL, start.index = 2, growth.cutoff = 0.05,
+  add.constant = 0, blank.value, start.index, growth.cutoff = 0.05,
   use.linear.param = F, use.loess = F, smooth.param=0.1,
   lagRange = NA, totalRange = NA, specRange = NA,
   points.to.remove = 0, remove.jumps = F, time.input = NA,
@@ -126,6 +126,11 @@ gcat.analysis.main = function(file.list, single.plate, layout.file = NULL,
   
   #  Capture the starting environment for debugging
   main.envir = c(as.list(environment()))
+  
+  #  Check blank value and start index
+  if (is.null(blank.value) && start.index==1) {
+    exception("", "If inoculation time point is 1, the user must specify a blank value")
+  }
 
     # MB: Not the best solution.
     if (is.na(time.input)) {

R/GCAT/R/class.well.R

@@ -306,6 +306,7 @@ setMethod("show", "well",
 #' @param  well.number the number of the well in an array of wells
 #' @param  ... additional arguments passed to the generic plot function
 #' 
+#' @export
 setMethod("plot",
           signature(x = "well", y="missing"),
           function (x, y, constant.added = 1.0, xlim = NULL, ylim = NULL,

R/GCAT/man/gcat.analysis.main.Rd

@@ -6,15 +6,14 @@
 \usage{
 gcat.analysis.main(file.list, single.plate, layout.file = NULL,
   out.dir = getwd(), graphic.dir = paste(out.dir, "/pics", sep = ""),
-  add.constant = 0, blank.value = NULL, start.index = 2,
-  growth.cutoff = 0.05, use.linear.param = F, use.loess = F,
-  smooth.param = 0.1, lagRange = NA, totalRange = NA, specRange = NA,
-  points.to.remove = 0, remove.jumps = F, time.input = NA,
-  plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,
-  multi.column.headers = c("Plate.ID", "Well", "OD", "Time"),
-  single.column.headers = c("", "A1"), layout.sheet.headers = c("Strain",
-  "Media Definition"), silent = T, verbose = F, return.fit = F,
-  overview.jpgs = T)
+  add.constant = 0, blank.value, start.index, growth.cutoff = 0.05,
+  use.linear.param = F, use.loess = F, smooth.param = 0.1,
+  lagRange = NA, totalRange = NA, specRange = NA, points.to.remove = 0,
+  remove.jumps = F, time.input = NA, plate.nrow = 8, plate.ncol = 12,
+  input.skip.lines = 0, multi.column.headers = c("Plate.ID", "Well", "OD",
+  "Time"), single.column.headers = c("", "A1"),
+  layout.sheet.headers = c("Strain", "Media Definition"), silent = T,
+  verbose = F, return.fit = F, overview.jpgs = T)
 }
 \arguments{
 \item{file.list}{A list of full paths to .csv files. all files must be in the same format (see <single.plate>)}
@@ -29,7 +28,7 @@ gcat.analysis.main(file.list, single.plate, layout.file = NULL,
 
 \item{add.constant}{A numeric constant that will be added to each curve before the log transform (defaults to 1)}
 
-\item{blank.value}{User can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well.}
+\item{blank.value}{User can enter a blank OD measurement for uninoculated wells. if NULL, assumes the first OD measurement of each well to be blank.}
 
 \item{start.index}{Which timepoint should be used as the first one after inoculation (defaults to the 2th one)}