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: 6.0.1
-Version: 5.0.2
 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,
@@ -127,6 +127,11 @@ 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)) {
       if (single.plate)

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,
+  add.constant = 0, blank.value, start.index, growth.cutoff = 0.05,
-  growth.cutoff = 0.05, use.linear.param = F, use.loess = F,
+  use.linear.param = F, use.loess = F, smooth.param = 0.1,
-  smooth.param = 0.1, lagRange = NA, totalRange = NA, specRange = NA,
+  lagRange = NA, totalRange = NA, specRange = NA, points.to.remove = 0,
-  points.to.remove = 0, remove.jumps = F, time.input = NA,
+  remove.jumps = F, time.input = NA, plate.nrow = 8, plate.ncol = 12,
-  plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,
+  input.skip.lines = 0, multi.column.headers = c("Plate.ID", "Well", "OD",
-  multi.column.headers = c("Plate.ID", "Well", "OD", "Time"),
+  "Time"), single.column.headers = c("", "A1"),
-  single.column.headers = c("", "A1"), layout.sheet.headers = c("Strain",
+  layout.sheet.headers = c("Strain", "Media Definition"), silent = T,
-  "Media Definition"), silent = T, verbose = F, return.fit = F,
+  verbose = F, return.fit = F, overview.jpgs = T)
-  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)}
 

Rails/app/models/assay.rb

@@ -139,7 +139,7 @@ class Assay
     # (4) start index (A Positive Integer Number)
     if 
       start_index == ''
-      self.start_index = 2
+      self.start_index = 1
     else  
       self.start_index.gsub(/\s+/, "")  # remove white spaces
       self.start_index = self.start_index.to_i
@@ -276,6 +276,7 @@ class Assay
     # (2) transformation. N value (A Real Number)
     R.assign "add.constant", self.transformation
     # R.assign "add.constant", 0
+
     # (3) blank value (A Real Number)
     if (self.blank_value == nil)
       R.eval "blank.value <- NULL"
@@ -284,8 +285,14 @@ class Assay
     else
       R.assign "blank.value", self.blank_value
     end
-    # (4) start index (A Positive Integer Number)
+
-    R.assign "start.index", self.start_index
+    # (4) start index (A Positive Integer Number).  Cannot be 1 if blank value is nil.
+    if(self.blank_value == nil && self.start_index == 1)
+      return {:error_message => "Error: inoculation timepoint cannot be 1 if using first OD reading as blank", :path => inputfile}
+    else 
+      R.assign "start.index", self.start_index
+    end
+    
     # (5) remove points [a space-separated list of points. Example: 2,3,4,5 (Positive Integer Number)]
     R.assign "points.to.remove", self.remove_points
     

Rails/app/views/assays/_form.html.erb

@@ -45,16 +45,17 @@
           </div>
         </li>
         <li>
-          <h3><span data-tooltip="OD value for blank well read. As the default option <NULL>, GCAT will automatically take the first OD reading of each well to be the blank.">Media background</span></h3>
+          <h3><span data-tooltip="OD value for blank well read">Media background</span></h3>
-          <%= f.radio_button(:blank_value, "zero", {:class => "user_enter3 user_enter3_no"}) %>
-          <%= f.label(:blank_value_zero, "0" ) %> <br/>
-          <%= f.radio_button(:blank_value, "default", {:class => "user_enter3 user_enter3_no"}) %>
-          <%= f.label(:blank_value_default, "Take the first OD reading of each well to be the blank") %><br>
           <%= f.radio_button(:blank_value, "user", {:checked => true, :class => "user_enter3 user_enter3_yes"}) %>
           <%= f.label(:blank_value_user, "User Input.") %>
           <div class="field optional_input3" style="display:none">
             <%= f.text_field :blank_value_input, :placeholder => 'Enter your OD blank value here' %>
           </div>
+          <br>
+          <%= f.radio_button(:blank_value, "default", {:class => "user_enter3 user_enter3_no"}) %>
+          <%= f.label(:blank_value_default, "Take the first OD reading of each well to be the blank") %><br>
+          <%= f.radio_button(:blank_value, "zero", {:class => "user_enter3 user_enter3_no"}) %>
+          <%= f.label(:blank_value_zero, "Set to 0" ) %>
         </li>
         <li>
           <h3><span data-tooltip="GCAT transforms optical density (OD) to log(x+δ). x = OD – Media background. Specify a value for n or choose from the defaults. Note: 0 is not recommended unless all wells contain many repeated measurements for initial density that can be used to accurately estimate the baseline density. See the user manual for more details.">OD Transform</span></h3>
@@ -84,8 +85,8 @@
           <h3><span data-tooltip="Enter the index of the timepoint at which the wells were inoculated with the culture. 
             " >Inoculation timepoint</span></h3>
           <div class="field">
-              <%= f.label :start_index, "Enter the timepoint index (positive integer only).  The default value is 2. "  %><br />
+              <%= f.label :start_index, "Enter the timepoint index (positive integer only).  The default value is 1. "  %><br />
-              <%= f.text_field(:start_index, :type => 'number', :min =>'1', :size => '3', :value => '2') %>
+              <%= f.text_field(:start_index, :type => 'number', :min =>'1', :size => '3', :value => '1') %>
           </div>
         </li>
         <li>