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Demo AUC

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master
Minh 9 years ago
parent 30e0658245
commit 329c63caef
14 changed files with 468 additions and 372 deletions
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27
R/GCAT/R/GCAT.main.R
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@ -110,6 +110,7 @@ global.version.number = packageDescription(pkg="GCAT")$Version
#' @param totalRange The heatmap specific range for the achieved growth on log scale. #' @param totalRange The heatmap specific range for the achieved growth on log scale.
#' @param totalODRange The heatmap specific range for the achieved growth on linear (OD) scale. #' @param totalODRange The heatmap specific range for the achieved growth on linear (OD) scale.
#' @param specRange The heatmap specific range for spec growth rate. #' @param specRange The heatmap specific range for spec growth rate.
#' @param sranges The 2 boundaries for calculating the area under the curve.
#' #'
#' @return Depending on return.fit setting, an array of fitted well objects or a list of output files #' @return Depending on return.fit setting, an array of fitted well objects or a list of output files
#' #'
@ -120,7 +121,7 @@ gcat.analysis.main = function(file.list, single.plate, layout.file = NULL,
use.linear.param = F, use.loess = F, smooth.param=0.1, use.linear.param = F, use.loess = F, smooth.param=0.1,
lagRange = NA, totalRange = NA, totalODRange = NA, specRange = NA, lagRange = NA, totalRange = NA, totalODRange = NA, specRange = NA,
points.to.remove = 0, remove.jumps = F, time.input = NA, points.to.remove = 0, remove.jumps = F, time.input = NA,
plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0, plate.nrow = 8, plate.ncol = 12, sranges = NA, input.skip.lines = 0,
multi.column.headers = c("Plate.ID", "Well", "OD", "Time"), single.column.headers = c("","A1"), multi.column.headers = c("Plate.ID", "Well", "OD", "Time"), single.column.headers = c("","A1"),
layout.sheet.headers = c("Strain", "Media Definition"), layout.sheet.headers = c("Strain", "Media Definition"),
silent = T, verbose = F, return.fit = F, overview.jpgs = T){ silent = T, verbose = F, return.fit = F, overview.jpgs = T){
@ -152,6 +153,16 @@ gcat.analysis.main = function(file.list, single.plate, layout.file = NULL,
} }
} }
if (!identical(sranges, NA)) {
sranges.string = paste(sranges, collapse = "-")
if (length(sranges) != 2)
exception("", paste("Should have 2 values for the bounds of integration. Bad range:", sranges.string))
if (sranges[2] < sranges[1])
exception("", paste("Bad range. The first range cannot be greater than the second:", sranges.string))
if (sranges[1] < 0 | sranges[2] < 0)
exception("", paste("Bad range. Either one of the range is negative:", sranges.string))
}
# MB: Now add.constant will always be 0. # MB: Now add.constant will always be 0.
# No need to check. # No need to check.
#if (add.constant < 0) #if (add.constant < 0)
@ -179,7 +190,7 @@ gcat.analysis.main = function(file.list, single.plate, layout.file = NULL,
use.linear.param=use.linear.param, use.loess=use.loess, smooth.param=smooth.param, use.linear.param=use.linear.param, use.loess=use.loess, smooth.param=smooth.param,
plate.nrow = plate.nrow, plate.ncol = plate.ncol, multi.column.headers = multi.column.headers, plate.nrow = plate.nrow, plate.ncol = plate.ncol, multi.column.headers = multi.column.headers,
single.column.headers = single.column.headers, layout.sheet.headers = layout.sheet.headers, single.column.headers = single.column.headers, layout.sheet.headers = layout.sheet.headers,
input.skip.lines = input.skip.lines, silent = silent, verbose = verbose), silent = T) input.skip.lines = input.skip.lines, silent = silent, verbose = verbose, sranges = sranges), silent = T)
# Return error message if the function fails. # Return error message if the function fails.
if(class(fitted.well.array) == "try-error") if(class(fitted.well.array) == "try-error")
@ -197,7 +208,7 @@ gcat.analysis.main = function(file.list, single.plate, layout.file = NULL,
growth.cutoff = growth.cutoff, add.constant = add.constant, blank.value = blank.value, start.index = start.index, growth.cutoff = growth.cutoff, add.constant = add.constant, blank.value = blank.value, start.index = start.index,
points.to.remove = points.to.remove, remove.jumps = remove.jumps, points.to.remove = points.to.remove, remove.jumps = remove.jumps,
lagRange = lagRange, specRange = specRange, totalRange = totalRange, totalODRange = totalODRange, lagRange = lagRange, specRange = specRange, totalRange = totalRange, totalODRange = totalODRange,
out.dir = out.dir, graphic.dir = graphic.dir, overview.jpgs=overview.jpgs, sranges = sranges, out.dir = out.dir, graphic.dir = graphic.dir, overview.jpgs=overview.jpgs,
use.linear.param=use.linear.param, use.loess=use.loess, plate.ncol = plate.ncol, plate.nrow = plate.nrow, use.linear.param=use.linear.param, use.loess=use.loess, plate.ncol = plate.ncol, plate.nrow = plate.nrow,
silent = silent, main.envir = main.envir), silent = T) silent = silent, main.envir = main.envir), silent = T)
@ -261,6 +272,7 @@ gcat.analysis.main = function(file.list, single.plate, layout.file = NULL,
#' @param layout.sheet.headers The headers of the layout file. #' @param layout.sheet.headers The headers of the layout file.
#' @param growth.model What growth model should be used? #' @param growth.model What growth model should be used?
#' @param backup.growth.model If the main growth model fails, the back up model will be used. #' @param backup.growth.model If the main growth model fails, the back up model will be used.
#' @param sranges The 2 boundaries for calculating the area under the curve.
#' @param silent Surpress all messages. #' @param silent Surpress all messages.
#' @param verbose Display all messages when analyzing each well. #' @param verbose Display all messages when analyzing each well.
#' #'
@ -270,7 +282,7 @@ gcat.fit.main = function(file.name, input.data = NULL, load.type = "csv", layout
normalize.method = "default", add.constant = 1, use.log = T, points.to.remove = 0, normalize.method = "default", add.constant = 1, use.log = T, points.to.remove = 0,
use.linear.param=F, use.loess=F, smooth.param=0.1, use.linear.param=F, use.loess=F, smooth.param=0.1,
fall.cutoff = -0.0025, growth.cutoff = 0.05, remove.jumps = F, fall.cutoff = -0.0025, growth.cutoff = 0.05, remove.jumps = F,
plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0, plate.nrow = 8, plate.ncol = 12, sranges = NA, input.skip.lines = 0,
multi.column.headers = c("Plate.ID", "Well", "OD", "Time"), single.column.headers = c("","A1"), multi.column.headers = c("Plate.ID", "Well", "OD", "Time"), single.column.headers = c("","A1"),
layout.sheet.headers = c("Strain", "Media Definition"), layout.sheet.headers = c("Strain", "Media Definition"),
growth.model = NA, backup.growth.model = NA, growth.model = NA, backup.growth.model = NA,
@ -452,7 +464,7 @@ gcat.fit.main = function(file.name, input.data = NULL, load.type = "csv", layout
# Return an error if there is a problem with model fitting # Return an error if there is a problem with model fitting
if (class(well.array) == "try-error") if (class(well.array) == "try-error")
stop("Error in <fit.model>: ", well.array) stop("Error in <fit.model>: ", well.array)
well.array = try(AUC_well(well.array, sranges[1], sranges[2], silent = silent))
if(!silent) cat("\ndone!\n") if(!silent) cat("\ndone!\n")
return(well.array) return(well.array)
} }
@ -495,11 +507,12 @@ gcat.fit.main = function(file.name, input.data = NULL, load.type = "csv", layout
#' @param totalODRange The heatmap specific range for the achieved growth on linear (OD) scale. #' @param totalODRange The heatmap specific range for the achieved growth on linear (OD) scale.
#' @param specRange The heatmap specific range for spec growth rate. #' @param specRange The heatmap specific range for spec growth rate.
#' @param main.envir starting environment of gcat.analysis.main(), captured as a list, printed out for debugging #' @param main.envir starting environment of gcat.analysis.main(), captured as a list, printed out for debugging
#' @param sranges The 2 boundaries for calculating the area under the curve.
#' #'
#' @return A list of output files if success. #' @return A list of output files if success.
gcat.output.main = function(fitted.well.array, out.prefix = "", source.file.list, upload.timestamp = NULL, gcat.output.main = function(fitted.well.array, out.prefix = "", source.file.list, upload.timestamp = NULL,
add.constant, blank.value, start.index, growth.cutoff, points.to.remove, remove.jumps, add.constant, blank.value, start.index, growth.cutoff, points.to.remove, remove.jumps,
out.dir = getwd(), graphic.dir = paste(out.dir,"/pics",sep = ""), overview.jpgs = T, out.dir = getwd(), graphic.dir = paste(out.dir,"/pics",sep = ""), overview.jpgs = T, sranges = NA,
use.linear.param=F, use.loess=F, lagRange = NA, totalRange = NA, totalODRange = NA, specRange = NA, use.linear.param=F, use.loess=F, lagRange = NA, totalRange = NA, totalODRange = NA, specRange = NA,
plate.nrow = 8, plate.ncol = 12, unlog = F, silent = T, main.envir){ plate.nrow = 8, plate.ncol = 12, unlog = F, silent = T, main.envir){
@ -571,7 +584,7 @@ gcat.output.main = function(fitted.well.array, out.prefix = "", source.file.list
graphic.files = try(pdf.by.plate(fitted.well.array, out.prefix=out.prefix, upload.timestamp = upload.timestamp, graphic.files = try(pdf.by.plate(fitted.well.array, out.prefix=out.prefix, upload.timestamp = upload.timestamp,
unlog=unlog,constant.added=add.constant,overview.jpgs=overview.jpgs, lagRange = lagRange, specRange = specRange, totalRange = totalRange, unlog=unlog,constant.added=add.constant,overview.jpgs=overview.jpgs, lagRange = lagRange, specRange = specRange, totalRange = totalRange,
totalODRange = totalODRange, plate.ncol = plate.ncol, plate.nrow = plate.nrow),silent=silent) totalODRange = totalODRange, sranges = sranges, plate.ncol = plate.ncol, plate.nrow = plate.nrow),silent=silent)
if (class(graphic.files) == "try-error") if (class(graphic.files) == "try-error")
stop("Error in <pdf.by.plate>: ", graphic.files) stop("Error in <pdf.by.plate>: ", graphic.files)

9
R/GCAT/R/class.well.R
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@ -53,6 +53,7 @@ setOldClass("loess")
#' @slot rss - residual sum of squares #' @slot rss - residual sum of squares
#' @slot loess - object returned by running loess on the normalized well data #' @slot loess - object returned by running loess on the normalized well data
#' @slot nls - object returned by running nls on the normalized well data #' @slot nls - object returned by running nls on the normalized well data
#' @slot auc - The area under the curve.
#' #'
#' @export #' @export
setClass("well", representation(position = "character", setClass("well", representation(position = "character",
@ -71,7 +72,8 @@ setClass("well", representation(position = "character",
inflection.time = "numeric", inflection.time = "numeric",
rss = "numeric", rss = "numeric",
loess = "loess", loess = "loess",
nls = "nls")) nls = "nls",
auc = "character"))
#' Accessors for the well class #' Accessors for the well class
#' #'
@ -304,13 +306,14 @@ setMethod("show", "well",
#' @param show.calc draw lines that illustrate growth curve parameters #' @param show.calc draw lines that illustrate growth curve parameters
#' @param draw.guess initial guess model. Drawn if specified #' @param draw.guess initial guess model. Drawn if specified
#' @param well.number the number of the well in an array of wells #' @param well.number the number of the well in an array of wells
#' @param sranges The boundaries to calculate the AUC.
#' @param ... additional arguments passed to the generic plot function #' @param ... additional arguments passed to the generic plot function
#' #'
#' @export #' @export
setMethod("plot", setMethod("plot",
signature(x = "well", y="missing"), signature(x = "well", y="missing"),
function (x, y, constant.added = 1.0, xlim = NULL, ylim = NULL, function (x, y, constant.added = 1.0, xlim = NULL, ylim = NULL,
well.number = NULL, scale = 1, number.points = T, draw.symbols = F, show.text = T, show.calc = T, draw.guess = NULL, ...) well.number = NULL, scale = 1, number.points = T, draw.symbols = F, show.text = T, show.calc = T, draw.guess = NULL, sranges = NA, ...)
{ {
# Determine the boundaries for the axes (if user did not specify them) # Determine the boundaries for the axes (if user did not specify them)
if(is.null(ylim)){ if(is.null(ylim)){
@ -347,7 +350,7 @@ setMethod("plot",
# Show calculated parameters if specified. # Show calculated parameters if specified.
if (show.calc) if (show.calc)
draw.calc.par(x, scale = scale * 0.5, constant.added = constant.added) draw.calc.par(x, scale = scale * 0.5, constant.added = constant.added, sranges = sranges)
# Draw initial guess if a model is specified. # Draw initial guess if a model is specified.
if (class(draw.guess) == "model"){ if (class(draw.guess) == "model"){

18
R/GCAT/R/fitted.calculations.R
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@ -340,3 +340,21 @@ inflection.time = function(well){
infl.index = which.max(dydt) infl.index = which.max(dydt)
t[infl.index] t[infl.index]
} }
# Calculate the area under the curve with the specified time range.
AUC_well <- function(well.array, a = 0, b = 1, silent = TRUE) {
for (i in 1:length(well.array)) {
f <- function(x) {well.eval(well.array[[i]], x)}
auc.string = try(integrate(f, a, b), silent = silent)
if (class(auc.string) == "try-error")
{
well.array[[i]]@auc = ""
if (!silent) print(paste("Cannot calculate the area at well: ", i))
}
else {
well.array[[i]]@auc = paste(abs(round(auc.string$value, digits = 3)), "with boundaries: (", a, ",", b, ")")
}
}
return (well.array)
}

20
R/GCAT/R/plot.fit.R
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@ -140,7 +140,7 @@ draw.text = function(input.well, scale = 0.5, xlim = 0, ylim = 0,...){
# color = green if empty, blue if inoculated, red if inoculated but has no growth or empty but has growth. # color = green if empty, blue if inoculated, red if inoculated but has no growth or empty but has growth.
col2 = "blue" col2 = "blue"
text2 = paste(input.well@fit.info, input.well@model.name, input.well@add.info, "\n", parameter.text(input.well)) text2 = paste(input.well@fit.info, input.well@model.name, input.well@add.info, "\n", parameter.text(input.well), "\n", "AUC: ", input.well@auc)
if (length(input.well@fit.par) == 0) # no fit if (length(input.well@fit.par) == 0) # no fit
col2 = "red" col2 = "red"
@ -196,7 +196,7 @@ draw.text = function(input.well, scale = 0.5, xlim = 0, ylim = 0,...){
# @details # @details
# \strong{show.num} - should curve parameters be labeled? # \strong{show.num} - should curve parameters be labeled?
# #
draw.calc.par = function(input.well, scale = 0.5, unlog = F, constant.added, show.num = T){ draw.calc.par = function(input.well, scale = 0.5, unlog = F, constant.added, show.num = T, sranges = NA){
# Don't do anything if well was not fit. # Don't do anything if well was not fit.
if (is.null(well.eval(input.well))) if (is.null(well.eval(input.well)))
@ -222,6 +222,14 @@ draw.calc.par = function(input.well, scale = 0.5, unlog = F, constant.added, sho
# ---- Specific growth rate ---- # # ---- Specific growth rate ---- #
lines(c(lag.x, inflection.time), c(lag.y, max.y), lty = 2, col = "red") lines(c(lag.x, inflection.time), c(lag.y, max.y), lty = 2, col = "red")
# MB: Drawing boundaries for the AUC.
if (!is.na(sranges))
{
#abline(v = sranges[1], lty = 1)
segments(sranges[1], baseline, sranges[1], well.eval(input.well, sranges[1]), lty = 1)
segments(sranges[2], baseline, sranges[2], well.eval(input.well, sranges[2]), lty = 1)
#abline(v = sranges[2], lty = 1)
}
# Blue dotted line at time of maximum growth, with text label for specific growth rate. # Blue dotted line at time of maximum growth, with text label for specific growth rate.
abline(v = inflection.time, lty = 2, lw = (scale^2)*2, col = "blue") abline(v = inflection.time, lty = 2, lw = (scale^2)*2, col = "blue")
@ -485,7 +493,7 @@ plate.overview = function(fitted.well.array, scale = 1, plate.ncol = 12, plate.n
view.fit = function(fitted.data, indices = 1:length(fitted.data), view.fit = function(fitted.data, indices = 1:length(fitted.data),
unlog = F, constant.added, xlim = NULL, ylim = NULL, display.legend = T, unlog = F, constant.added, xlim = NULL, ylim = NULL, display.legend = T,
show.text = T, show.calc = T, draw.guess = NULL, draw.symbols = F, number.points = T, show.text = T, show.calc = T, draw.guess = NULL, draw.symbols = F, number.points = T,
user.advance = T, show.residuals = F, scale = 1,...){ user.advance = T, show.residuals = F, scale = 1, sranges = sranges,...){
if(!is.array(fitted.data)) if(!is.array(fitted.data))
fitted.data = list(fitted.data) fitted.data = list(fitted.data)
@ -530,7 +538,7 @@ view.fit = function(fitted.data, indices = 1:length(fitted.data),
# plot the well # plot the well
fitted.well = fitted.data[[well.number]] fitted.well = fitted.data[[well.number]]
plot(x=fitted.well, constant.added = constant.added, xlim = xlim, ylim = ylim, plot(x=fitted.well, constant.added = constant.added, xlim = xlim, ylim = ylim,
unlog = unlog, well.number = well.number, scale = scale, number.points = T, draw.symbols = F, show.text = T, show.calc = T, draw.guess = NULL, ...) unlog = unlog, well.number = well.number, scale = scale, number.points = T, draw.symbols = F, show.text = T, show.calc = T, draw.guess = NULL, sranges = sranges, ...)
if(user.advance) if(user.advance)
cat("\n[", well.number, "] ", plate.name(fitted.well), " ", well.name(fitted.well), ".", sep = "") cat("\n[", well.number, "] ", plate.name(fitted.well), " ", well.name(fitted.well), ".", sep = "")
@ -616,7 +624,7 @@ well.fit.legend = function(xlim, ylim, scale = 1, constant.added){
# Generate pdf files # Generate pdf files
pdf.by.plate = function(fitted.data, out.prefix = "", upload.timestamp = NULL, pdf.by.plate = function(fitted.data, out.prefix = "", upload.timestamp = NULL,
out.dir = getwd(), unlog = F, constant.added, silent = T, overview.jpgs = T, plate.ncol = 12, plate.nrow = 8, out.dir = getwd(), unlog = F, constant.added, silent = T, overview.jpgs = T, plate.ncol = 12, plate.nrow = 8,
lagRange = NA, specRange = NA, totalRange = NA, totalODRange = NA, ...){ lagRange = NA, specRange = NA, totalRange = NA, totalODRange = NA, sranges = sranges,...){
# Prepare timestamp for addition to output file names. # Prepare timestamp for addition to output file names.
filename.timestamp = strftime(upload.timestamp, format="_%Y-%m-%d_%H.%M.%S") filename.timestamp = strftime(upload.timestamp, format="_%Y-%m-%d_%H.%M.%S")
@ -678,7 +686,7 @@ pdf.by.plate = function(fitted.data, out.prefix = "", upload.timestamp = NULL,
pdf(pdf.name, title = paste("R Graphics output for plate", plate.ID)) pdf(pdf.name, title = paste("R Graphics output for plate", plate.ID))
# Call <view.fit> to draw each well on the plate to the pdf. # Call <view.fit> to draw each well on the plate to the pdf.
view.fit.out = try(view.fit(fitted.data, indices = plate.indices, unlog=unlog, constant.added=constant.added, user.advance=F,...),silent=T) view.fit.out = try(view.fit(fitted.data, indices = plate.indices, unlog=unlog, constant.added=constant.added, user.advance=F, sranges = sranges,...),silent=T)
if(class(view.fit.out) == "try-error") if(class(view.fit.out) == "try-error")
stop("Error in <view.fit>: ", view.fit.out) stop("Error in <view.fit>: ", view.fit.out)

20
R/GCAT/man/GCAT.Rd
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@ -0,0 +1,20 @@
% Generated by roxygen2 (4.1.1): do not edit by hand
% Please edit documentation in R/GCAT.main.R
\docType{package}
\name{GCAT}
\alias{GCAT}
\alias{GCAT-package}
\title{GCAT: Growth Curve Analysis Tool}
\description{
Mathematical modeling and parameter estimation of high volume microbial growth data.
}
\details{
GCAT input is in .csv format. GCAT analysis is accessed using \code{\link{gcat.analysis.main}}
GCAT utilizes the \code{\link[stats]{nls}} function in the R stats package to fit logistic, Gompertz and Richards models to growth curve
data. Best model is selected automatically. Alternatively, the user may choose LOESS local regression fits, implemented using
\code{\link[stats]{loess}} function in the R stats package
Internally, the data are stored in an array of \linkS4class{well} objects
}

4
R/GCAT/man/gcat.analysis.main.Rd
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@ -10,7 +10,7 @@ gcat.analysis.main(file.list, single.plate, layout.file = NULL,
use.linear.param = F, use.loess = F, smooth.param = 0.1, use.linear.param = F, use.loess = F, smooth.param = 0.1,
lagRange = NA, totalRange = NA, totalODRange = NA, specRange = NA, lagRange = NA, totalRange = NA, totalODRange = NA, specRange = NA,
points.to.remove = 0, remove.jumps = F, time.input = NA, points.to.remove = 0, remove.jumps = F, time.input = NA,
plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0, plate.nrow = 8, plate.ncol = 12, sranges = NA, input.skip.lines = 0,
multi.column.headers = c("Plate.ID", "Well", "OD", "Time"), multi.column.headers = c("Plate.ID", "Well", "OD", "Time"),
single.column.headers = c("", "A1"), layout.sheet.headers = c("Strain", single.column.headers = c("", "A1"), layout.sheet.headers = c("Strain",
"Media Definition"), silent = T, verbose = F, return.fit = F, "Media Definition"), silent = T, verbose = F, return.fit = F,
@ -59,6 +59,8 @@ gcat.analysis.main(file.list, single.plate, layout.file = NULL,
\item{plate.ncol}{The number of columns in a plate.} \item{plate.ncol}{The number of columns in a plate.}
\item{sranges}{The 2 boundaries for calculating the area under the curve.}
\item{input.skip.lines}{If specified, this number of lines shall be skipped from the top when reading the input file with read.csv} \item{input.skip.lines}{If specified, this number of lines shall be skipped from the top when reading the input file with read.csv}
\item{multi.column.headers}{The headers of the result tabular data when analyzing multiple plates at once.} \item{multi.column.headers}{The headers of the result tabular data when analyzing multiple plates at once.}

4
R/GCAT/man/gcat.fit.main.Rd
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@ -10,7 +10,7 @@ gcat.fit.main(file.name, input.data = NULL, load.type = "csv",
add.constant = 1, use.log = T, points.to.remove = 0, add.constant = 1, use.log = T, points.to.remove = 0,
use.linear.param = F, use.loess = F, smooth.param = 0.1, use.linear.param = F, use.loess = F, smooth.param = 0.1,
fall.cutoff = -0.0025, growth.cutoff = 0.05, remove.jumps = F, fall.cutoff = -0.0025, growth.cutoff = 0.05, remove.jumps = F,
plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0, plate.nrow = 8, plate.ncol = 12, sranges = NA, input.skip.lines = 0,
multi.column.headers = c("Plate.ID", "Well", "OD", "Time"), multi.column.headers = c("Plate.ID", "Well", "OD", "Time"),
single.column.headers = c("", "A1"), layout.sheet.headers = c("Strain", single.column.headers = c("", "A1"), layout.sheet.headers = c("Strain",
"Media Definition"), growth.model = NA, backup.growth.model = NA, "Media Definition"), growth.model = NA, backup.growth.model = NA,
@ -63,6 +63,8 @@ By default(0) none are marked for removal.}
\item{plate.ncol}{The number of columns in the input files.} \item{plate.ncol}{The number of columns in the input files.}
\item{sranges}{The 2 boundaries for calculating the area under the curve.}
\item{input.skip.lines}{If specified, this number of lines shall be skipped from the top when reading the input file with read.csv} \item{input.skip.lines}{If specified, this number of lines shall be skipped from the top when reading the input file with read.csv}
\item{multi.column.headers}{The headers of the column when analyzing multiple plates.} \item{multi.column.headers}{The headers of the column when analyzing multiple plates.}

8
R/GCAT/man/gcat.output.main.Rd
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@ -8,9 +8,9 @@ gcat.output.main(fitted.well.array, out.prefix = "", source.file.list,
upload.timestamp = NULL, add.constant, blank.value, start.index, upload.timestamp = NULL, add.constant, blank.value, start.index,
growth.cutoff, points.to.remove, remove.jumps, out.dir = getwd(), growth.cutoff, points.to.remove, remove.jumps, out.dir = getwd(),
graphic.dir = paste(out.dir, "/pics", sep = ""), overview.jpgs = T, graphic.dir = paste(out.dir, "/pics", sep = ""), overview.jpgs = T,
use.linear.param = F, use.loess = F, lagRange = NA, totalRange = NA, sranges = NA, use.linear.param = F, use.loess = F, lagRange = NA,
totalODRange = NA, specRange = NA, plate.nrow = 8, plate.ncol = 12, totalRange = NA, totalODRange = NA, specRange = NA, plate.nrow = 8,
unlog = F, silent = T, main.envir) plate.ncol = 12, unlog = F, silent = T, main.envir)
} }
\arguments{ \arguments{
\item{fitted.well.array}{A list of fitted well objects.} \item{fitted.well.array}{A list of fitted well objects.}
@ -42,6 +42,8 @@ If NULL, defaults to the value of the first OD measurement of each well.}
\item{overview.jpgs}{should jpgs be generated for each plate with the overview graphic? \item{overview.jpgs}{should jpgs be generated for each plate with the overview graphic?
This is for backwards compatibility with the old web server.} This is for backwards compatibility with the old web server.}
\item{sranges}{The 2 boundaries for calculating the area under the curve.}
\item{use.linear.param}{linear parameter is used or not?} \item{use.linear.param}{linear parameter is used or not?}
\item{use.loess}{Is LOESS model going to be used?} \item{use.loess}{Is LOESS model going to be used?}

4
R/GCAT/man/plot-well-missing-method.Rd
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@ -8,7 +8,7 @@
\S4method{plot}{well,missing}(x, y, constant.added = 1, xlim = NULL, \S4method{plot}{well,missing}(x, y, constant.added = 1, xlim = NULL,
ylim = NULL, well.number = NULL, scale = 1, number.points = T, ylim = NULL, well.number = NULL, scale = 1, number.points = T,
draw.symbols = F, show.text = T, show.calc = T, draw.guess = NULL, draw.symbols = F, show.text = T, show.calc = T, draw.guess = NULL,
...) sranges = NA, ...)
} }
\arguments{ \arguments{
\item{x}{object of class well} \item{x}{object of class well}
@ -35,6 +35,8 @@
\item{draw.guess}{initial guess model. Drawn if specified} \item{draw.guess}{initial guess model. Drawn if specified}
\item{sranges}{The boundaries to calculate the AUC.}
\item{...}{additional arguments passed to the generic plot function} \item{...}{additional arguments passed to the generic plot function}
} }
\description{ \description{

2
R/GCAT/man/well-class.Rd
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@ -44,5 +44,7 @@ Class that contains well data
\item{\code{loess}}{- object returned by running loess on the normalized well data} \item{\code{loess}}{- object returned by running loess on the normalized well data}
\item{\code{nls}}{- object returned by running nls on the normalized well data} \item{\code{nls}}{- object returned by running nls on the normalized well data}
\item{\code{auc}}{- The area under the curve.}
}} }}

2
R/GCAT/tests/YPDAFEXglucoseTests_2-25-10__defaults.R
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@ -13,7 +13,7 @@ time.input=1/3600
out = gcat.analysis.main(file.list = INPUT.FILE, single.plate = T, layout.file = NULL, out = gcat.analysis.main(file.list = INPUT.FILE, single.plate = T, layout.file = NULL,
out.dir = OUTPUT.DIR, graphic.dir = OUTPUT.DIR, out.dir = OUTPUT.DIR, graphic.dir = OUTPUT.DIR,
add.constant = 1, blank.value = NULL, start.index = 2, growth.cutoff = 0.05, add.constant = 1, blank.value = NULL, start.index = 2, growth.cutoff = 0.05,
use.linear.param=F, use.loess=F, smooth.param=0.1, use.linear.param=F, use.loess=F, smooth.param=0.1, sranges = c(5, 10),
points.to.remove = integer(), remove.jumps = F, time.input=time.input, points.to.remove = integer(), remove.jumps = F, time.input=time.input,
silent = F, verbose = T, return.fit = T, overview.jpgs = T) silent = F, verbose = T, return.fit = T, overview.jpgs = T)

2
Rails/app/assets/stylesheets/gcat.css.scss
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@ -81,7 +81,7 @@ a:visited { color: #428bca !important;}
/* MB: 1 option in GCAT. */ /* MB: 1 option in GCAT. */
#options li { #options li {
float: left; float: left;
width: 33%; width: 45%;
padding: 0 100px 0 0; padding: 0 100px 0 0;
} }

19
Rails/app/models/assay.rb
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@ -34,7 +34,7 @@ class Assay
extend ActiveModel::Naming extend ActiveModel::Naming
attr_accessor :input_file, :blank_value, :blank_value_input, :start_index, :remove_points, :remove_jumps, :plate_type, attr_accessor :input_file, :blank_value, :blank_value_input, :start_index, :remove_points, :remove_jumps, :plate_type,
:plate_dimensions_row, :plate_dimensions_column, :timestamp_format, :growth_threshold, :layout_file,:filename,:content_type, :model, :loess_input, :console_out, :specg_min, :plate_dimensions_row, :plate_dimensions_column, :timestamp_format, :growth_threshold, :layout_file,:filename,:content_type, :model, :loess_input, :console_out, :specg_min,
:specg_max, :totg_min, :totg_max, :totg_OD_min, :totg_OD_max, :lagT_min, :lagT_max,:transformation, :transformation_input :specg_max, :totg_min, :totg_max, :totg_OD_min, :totg_OD_max, :lagT_min, :lagT_max,:transformation, :transformation_input, :range_a, :range_b
# (1) Validation of input data file # (1) Validation of input data file
@ -189,6 +189,12 @@ class Assay
self.lagT_min = Float(self.lagT_min) self.lagT_min = Float(self.lagT_min)
end end
# (8) Integration bound
if (self.range_a != '' && self.range_a != '')
self.range_a = Float(self.range_a)
self.range_b = Float(self.range_b)
end
############################################################################################ ############################################################################################
@ -381,11 +387,20 @@ class Assay
R.eval 'lagRange <- NA' R.eval 'lagRange <- NA'
end end
# Integration bound.
if (self.range_a != '' && self.range_b != '')
R.assign 'range_a', self.range_a
R.assign 'range_b', self.range_b
R.eval "sranges <- c(range_a, range_b)"
else
R.eval "sranges <- NA"
end
# This block evaluates the files (csv or xlsx, single.plate or multiple.plate) # This block evaluates the files (csv or xlsx, single.plate or multiple.plate)
R.eval ('R_file_return_value <- gcat.analysis.main(file, single.plate, layout.file, out.dir=out.dir, graphic.dir = out.dir, add.constant, blank.value, R.eval ('R_file_return_value <- gcat.analysis.main(file, single.plate, layout.file, out.dir=out.dir, graphic.dir = out.dir, add.constant, blank.value,
start.index, growth.cutoff, use.linear.param=use.linear.param, use.loess=use.loess, smooth.param=smooth.param, start.index, growth.cutoff, use.linear.param=use.linear.param, use.loess=use.loess, smooth.param=smooth.param,
lagRange = lagRange, totalRange = totalRange, totalODRange = totalODRange, specRange = specRange, lagRange = lagRange, totalRange = totalRange, totalODRange = totalODRange, specRange = specRange,
points.to.remove = points.to.remove, remove.jumps, time.input, plate.nrow = 8, points.to.remove = points.to.remove, remove.jumps, time.input, plate.nrow = 8, sranges = sranges,
plate.ncol = 12, input.skip.lines = 0, multi.column.headers = c("Plate.ID", "Well", "OD", "Time"), single.column.headers = c("","A1"), 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)') layout.sheet.headers = c("Strain", "Media Definition"), silent = T, verbose = F, return.fit = F, overview.jpgs = T)')

9
Rails/app/views/assays/_form.html.erb
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@ -154,6 +154,15 @@
<%= f.text_field(:lagT_max, :size => '5') %> <%= f.text_field(:lagT_max, :size => '5') %>
</div> </div>
</li> </li>
<li>
<h3><span data-tooltip="Select value ranges to calculate the area under the curve">Integration ranges</span></h3>
<div class="field">
<%= f.label "Enter the time range" %><br />
<%= f.text_field :range_a, :size => '5' %>
<%= f.label "-" %>
<%= f.text_field :range_b, :size => '5' %>
</div>
</li>
<div class="actions" style="margin-top:30px; clear:both;"> <div class="actions" style="margin-top:30px; clear:both;">
<%= f.submit %> <%= f.submit %>
</div> </div>

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