Yury V Bukhman
9 years ago
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67544a10e6
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library(GCAT)
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library(GCAT)
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library(GCAT)
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source('~/Documents/GCAT4_old/trunk/R/GCAT/R/addingParams.R')
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library(GCAT)
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source('~/Documents/GCAT4_old/trunk/R/GCAT/R/addingParams.R')
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t
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warnings()
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library(GCAT)
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source('~/Documents/GCAT4_old/trunk/R/GCAT/R/addingParams.R')
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warnings()
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library(GCAT)
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source('~/Documents/GCAT4_old/trunk/R/GCAT/R/addingParams.R')
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warnings()
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library(GCAT)
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source('~/Documents/GCAT4_old/trunk/R/GCAT/R/addingParams.R')
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library(GCAT)
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library(GCAT)
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library("GCAT")
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library("codetools")
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checkUsagePackage("GCAT")
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library(GCAT)
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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t
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checkUsagePackage("GCAT")
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library("codetoolds")
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library("codetoolss")
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library("codetools")
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checkUsagePackage("GCAT")
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library(GCAT)
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library("codetools")
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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t
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checkUsagePackage("GCAT")
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/fit.model.R')
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library(GCAT)
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checkUsagePackage("GCAT")
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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t
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checkUsagePackage("GCAT")
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source('~/Documents/GCAT4/trunk/R/GCAT/R/class.model.R')
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library(GCAT)
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checkUsagePackage("GCAT")
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library(GCAT)
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checkUsagePackage("GCAT")
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library(GCAT)
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checkUsagePackage("GCAT")
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?? checkusagePackage
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checkUsagePackage("GCAT", all + T)
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checkUsagePackage("GCAT", all = T)
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checkUsagePackage("GCAT")
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checkUsagePackage("GCAT")
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source('~/Documents/GCAT4/trunk/R/GCAT/R/plot.fit.R')
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library(GCAT)
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checkUsagePackage("GCAT")
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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t
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t
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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t
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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t
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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t
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source('~/Documents/GCAT4/trunk/R/GCAT/R/plot.fit.R')
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/plot.fit.R')
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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t
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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t
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library(GCAT)
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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t
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library(GCAT)
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library(GCAT)
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library(GCAT)
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/table2well.R')
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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library(GCAT)
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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t
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library(GCAT)
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library(GCAT)
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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t
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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t
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library(GCAT)
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library(GCAT)
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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t
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library("codetools")
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library("GCAT")
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checkUsagePackage(GCAT)
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checkUsagePackage("GCAT)
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checkUsagePackage("GCAT")
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checkUsagePackage("GCAT")
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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t
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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t
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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t
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R')
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t
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checkUsagePack(GCAT)
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checkUsagePackage(GCAT)
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checkUsagePackage("GCAT")
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library(GCAT)
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library(GCAT)
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library(GCAT)
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/normalize.and.transform.R')
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library(GCAT)
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library(GCAT)
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library(GCAT)
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library(GCAT)
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library(GCAT)
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library(GCAT)
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library(GCAT)
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source('~/Documents/GCAT4/trunk/R/GCAT/R/plot.fit.R')
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library(GCAT)
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library(GCAT)
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library(GCAT)
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?? plot
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? plot
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library(GCAT)
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library(GCAT)
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library(GCAT)
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library(GCAT)
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library(GCAT)
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library(GCAT)
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library(GCAT)
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library(GCAT)
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library(GCAT)
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library(GCAT)
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library("codetools")
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checkPackageUsage("GCAT")
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checkUsagePackage("GCAT")
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checkUsagePackage("GCAT", all = T)
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auto_roxygenize_for_build_and_reload="1"
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auto_roxygenize_for_build_package="1"
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auto_roxygenize_for_check="1"
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makefile_args=""
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{
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"contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, \n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see <http://www.gnu.org/licenses/>.\n\n# Wrapper for sapply to use lapply over an array, conserving the dimensions.\naapply = function(x, FUN,...){\n dim.values = dim(x)\n\tdim.names = dimnames(x)\n\tx = lapply(x, function(x){FUN(x,...)})\n\tdim(x) = dim.values\n\tdimnames(x) = dim.names\n\treturn(x)\n\t}\n\n# A function to manually create an unchecked exception.\nexception = function(class, msg)\n{\n cond <- simpleError(msg)\n class(cond) <- c(class, \"MyException\", class(cond))\n stop(cond)\n}\n",
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"created" : 1425413273698.000,
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"lastKnownWriteTime" : 1424208963,
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"path" : "~/Documents/GCAT4/trunk/R/GCAT/R/misc.R",
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"project_path" : "R/misc.R",
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"properties" : {
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},
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"source_on_save" : false,
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"type" : "r_source"
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}
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{
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"contents" : "# Default NAMESPACE created by R\n# Remove the previous line if you edit this file\n\n# Export all names\nexportPattern(\".\")\n\n# Import all packages listed as Imports or Depends\nimport(\"pheatmap\", \"gplots\")\n",
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"created" : 1428439772005.000,
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"dirty" : false,
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"encoding" : "UTF-8",
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"hash" : "749067415",
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"id" : "907B51DB",
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"lastKnownWriteTime" : 1423260997,
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"path" : "~/Documents/GCAT4/trunk/R/GCAT/NAMESPACE",
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"project_path" : "NAMESPACE",
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"properties" : {
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},
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"source_on_save" : false,
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"type" : "r_namespace"
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}
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{
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"contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,\n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see <http://www.gnu.org/licenses/>.\n########################################################################\n# #\n# <model> class definition and functions. Objects contain equations #\n# and other information for parameterized growth curve models. #\n# #\n########################################################################\nsetClass(\"model\", representation(name = \"character\",\n expression = \"expression\",\n formula = \"formula\",\n guess = \"function\"))\n# Slots:\n# name - a simple description of the model.\n# expression - an object of class \"expression\" that evaluates the response (transformed OD) with respect to the variable Time.\n# formula - same as expression, but with y as the response.\n# guess - a function that computes initial guesses for the parameters given a well object with a valid \"screen.data\" slot\n# containing useable OD values and slope estimates\n# --------------------------------------------------------------------\n###################### BEGIN PROTOTYPING ACCESSOR METHODS##############\n\n# Minh: Let this code fragment be F1.\nif (!isGeneric(\"getName\")){\n if (is.function(\"getName\"))\n fun <- getName\n else\n fun <- function(object) standardGeneric(\"getName\")\n setGeneric(\"getName\", fun)\n}\n# End of F1\nsetMethod(\"getName\", \"model\", function(object) object@name)\n\n# Minh: Let this line be F2.\nsetGeneric(\"getExpression\", function(object){standardGeneric(\"getExpression\")})\n# Question: How is F1 different from F2?\n\nsetMethod(\"getExpression\", \"model\",\n function(object){\n return(object@expression)\n })\n\nsetGeneric(\"getFormula\", function(object){standeardGeneric(\"getFormula\")})\nsetMethod(\"getFormula\", \"model\", \n function(object){\n return(object@formula)\n })\n\nsetGeneric(\"getGuess\", function(object){standeardGeneric(\"getGuess\")})\nsetMethod(\"getGuess\", \"model\", \n function(object){\n return(object@guess)\n })\n######################## ENG PROTOTYPING ########################\n\n# Function to create a new model\n#' Model \n#' \n#' Function to create a new model \n#' @param name The name of the model \n#' @param expression Expression of the model \n#' @param formula The formula of this model \n#' @param guess The guess of this model \n#' @return The new model \nmodel = function(name, expression, formula, guess){\n new(\"model\", name = name, expression = expression, formula = formula, guess = guess)\n}\n\nloess.g = function(well,smooth.param=0.75){\n #data = data.from(well)\n #growth = data[,2]\n #Time = data[,1]\n Time = data.from(well)[,1]\n \n # predicted growth values to be used in estimating growth curve parameters\n loess.fit = loess(data.from(well)[,2]~Time,span=smooth.param)\n t = seq(from = min(Time), to = max(Time), by = (max(Time)-min(Time))/1000)\n y = predict(loess.fit, data.frame(Time=t))\n attr(y,\"names\") = NULL # need to remove the names to prevent them from showing up in the returned vector\n \n # Remove any data points where y has not been estimated\n filt = is.finite(y)\n t = t[filt]\n y = y[filt] # remove any NA etc\n \n # specific growth using loess to find max derivative\n delta.t = diff(t)\n dydt = diff(y)/delta.t\n u = max(dydt)\n \n # lower and upper asymptotes\n b = min(y)\n A = max(y) - min(y)\n \n # inflection point\n inflection.pt.index = which.max(dydt)\n inflection.time = t[inflection.pt.index]\n inflection.y = y[inflection.pt.index]\n \n # lag time\n lam = inflection.time - (inflection.y-b)/u\n \n # Return named array of estimates\n c(A = A, b = b, lam = lam, u = u)\n}\n\n\n",
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"path" : "~/Documents/GCAT4/trunk/R/GCAT/R/class.model.R",
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"project_path" : "R/class.model.R",
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"properties" : {
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||||||
},
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"source_on_save" : false,
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"type" : "r_source"
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}
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{
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"contents" : "setwd(\"~/Downloads/\")\nfile.list = file.name = \"YPDAFEXglucoseTests_2-25-10.csv\"\nlayout.file = \"YPDAFEXglucoseTests_2-25-10_Layout.csv\"\nsingle.plate = T\nout.dir = getwd()\ngraphic.dir = paste(out.dir, \"/pics\", sep = \"\")\nadd.constant = 1\nblank.value = NULL\nstart.index = 2\ngrowth.cutoff = 0.05\nuse.linear.param = F\nuse.loess = F\nsmooth.param = 0.6\npoints.to.remove = 0\nremove.jumps = F\nsilent = F\nverbose = T\nreturn.fit = F\noverview.jpgs = T\nplate.nrow = 8\nplate.ncol = 12\ninput.skip.lines = 0\nmulti.column.headers = c(\"Plate ID\", \"Well\", \"OD\", \"Time\")\nsingle.column.headers = c(\"\",\"A1\")\nlayout.sheet.headers = c(\"Strain\", \"Media Definition\")\n\nt = gcat.analysis.main(file.list, single.plate, layout.file = NULL, \n out.dir = getwd(), graphic.dir = paste(out.dir, \"/pics\", sep = \"\"), \n add.constant = 1, blank.value = NULL, start.index = 2, growth.cutoff = 0.05,\n use.linear.param=use.linear.param, use.loess=use.loess, smooth.param=0.1,\n points.to.remove = 0, remove.jumps = F, time.input = NA,\n plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,\n multi.column.headers = c(\"Plate.ID\", \"Well\", \"OD\", \"Time\"), single.column.headers = c(\"\",\"A1\"), \n layout.sheet.headers = c(\"Strain\", \"Media Definition\"),\n silent = F, verbose = F, return.fit = F, overview.jpgs = T)\n",
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"properties" : {
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|
|||||||
{
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|
||||||
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|
||||||
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|
|||||||
~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FNAMESPACE="972C75E0"
|
|
||||||
~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2FGCAT.main.R="11120BC5"
|
|
||||||
~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2FaddingParams.R="54A894D0"
|
|
||||||
~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Fclass.model.R="9127986F"
|
|
||||||
~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Fclass.well.R="8250000E"
|
|
||||||
~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Ffit.model.R="3F8DCF42"
|
|
||||||
~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Ffitted.calculations.R="E533697B"
|
|
||||||
~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Fmisc.R="8341E8EB"
|
|
||||||
~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Fnormalize.and.transform.R="EDBD9DE"
|
|
||||||
~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Fplot.fit.R="2E01469A"
|
|
||||||
~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Fslope.analysis.R="4E0B0FCA"
|
|
||||||
~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Ftable.output.R="B005EA5F"
|
|
||||||
~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Ftable2well.R="A3297EED"
|
|
||||||
~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2Fman%2Fgcat.load.data.Rd="2A2D32C6"
|
|
||||||
~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2FGCAT.main.R="61AC4784"
|
|
||||||
~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2FaddingParams.R="DEDB5126"
|
|
||||||
~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2Fclass.model.R="8CEE19EC"
|
|
||||||
~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2Ffit.model.R="9D1E246E"
|
|
||||||
@ -1,8 +1,24 @@
|
|||||||
# Default NAMESPACE created by R
|
# Generated by roxygen2 (4.1.1): do not edit by hand
|
||||||
# Remove the previous line if you edit this file
|
|
||||||
|
|
||||||
# Export all names
|
export(gcat.analysis.main)
|
||||||
exportPattern(".")
|
exportClasses(well)
|
||||||
|
exportMethods(getAddInfo)
|
||||||
# Import all packages listed as Imports or Depends
|
exportMethods(getCurPar)
|
||||||
import("pheatmap", "gplots")
|
exportMethods(getEquation)
|
||||||
|
exportMethods(getFitErr)
|
||||||
|
exportMethods(getFitInfo)
|
||||||
|
exportMethods(getFitPar)
|
||||||
|
exportMethods(getInflectionTime)
|
||||||
|
exportMethods(getLoess)
|
||||||
|
exportMethods(getModelName)
|
||||||
|
exportMethods(getNorm)
|
||||||
|
exportMethods(getPosition)
|
||||||
|
exportMethods(getRSS)
|
||||||
|
exportMethods(getScreenData)
|
||||||
|
exportMethods(getStartIndex)
|
||||||
|
exportMethods(getUseLog)
|
||||||
|
exportMethods(getWellInfo)
|
||||||
|
exportMethods(getnls)
|
||||||
|
import(gplots)
|
||||||
|
import(methods)
|
||||||
|
import(pheatmap)
|
||||||
|
|||||||
@ -1,17 +0,0 @@
|
|||||||
Version: 1.0
|
|
||||||
|
|
||||||
RestoreWorkspace: Default
|
|
||||||
SaveWorkspace: Default
|
|
||||||
AlwaysSaveHistory: Default
|
|
||||||
|
|
||||||
EnableCodeIndexing: Yes
|
|
||||||
UseSpacesForTab: Yes
|
|
||||||
NumSpacesForTab: 2
|
|
||||||
Encoding: UTF-8
|
|
||||||
|
|
||||||
RnwWeave: Sweave
|
|
||||||
LaTeX: pdfLaTeX
|
|
||||||
|
|
||||||
BuildType: Package
|
|
||||||
PackageInstallArgs: --no-multiarch --with-keep.source
|
|
||||||
PackageRoxygenize: rd
|
|
||||||
File diff suppressed because one or more lines are too long
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|
|||||||
{
|
|
||||||
"contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,\n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see <http://www.gnu.org/licenses/>.\n########################################################################\n# #\n# <model> class definition and functions. Objects contain equations #\n# and other information for parameterized growth curve models. #\n# #\n########################################################################\nsetClass(\"model\", representation(name = \"character\",\n expression = \"expression\",\n formula = \"formula\",\n guess = \"function\"))\n# Slots:\n# name - a simple description of the model.\n# expression - an object of class \"expression\" that evaluates the response (transformed OD) with respect to the variable Time.\n# formula - same as expression, but with y as the response.\n# guess - a function that computes initial guesses for the parameters given a well object with a valid \"screen.data\" slot\n# containing useable OD values and slope estimates\n# --------------------------------------------------------------------\n# Function to create a new model \t \n#' Model \n#' \n#' Function to create a new model \n#' @param name The name of the model \n#' @param expression Expression of the model \n#' @param formula The formula of this model \n#' @param guess The guess of this model \n#' @return The new model \nmodel = function(name, expression, formula, guess){\n new(\"model\", name = name, expression = expression, formula = formula, guess = guess)\n}\n\nloess.g = function(well,smooth.param=0.75){\n data = data.from(well)\n growth = data[,2]\n Time = data[,1]\n \n # predicted growth values to be used in estimating growth curve parameters\n loess.fit = loess(growth~Time,span=smooth.param)\n t = seq(from = min(Time), to = max(Time), by = (max(Time)-min(Time))/1000)\n y = predict(loess.fit, data.frame(Time=t))\n attr(y,\"names\") = NULL # need to remove the names to prevent them from showing up in the returned vector\n \n # Remove any data points where y has not been estimated\n filt = is.finite(y)\n t = t[filt]\n y = y[filt] # remove any NA etc\n \n # specific growth using loess to find max derivative\n delta.t = diff(t)\n dydt = diff(y)/delta.t\n u = max(dydt)\n \n # lower and upper asymptotes\n b = min(y)\n A = max(y) - min(y)\n \n # inflection point\n inflection.pt.index = which.max(dydt)\n inflection.time = t[inflection.pt.index]\n inflection.y = y[inflection.pt.index]\n \n # lag time\n lam = inflection.time - (inflection.y-b)/u\n \n # Return named array of estimates\n c(A = A, b = b, lam = lam, u = u)\n}\n\n\n",
|
|
||||||
"created" : 1423869204555.000,
|
|
||||||
"dirty" : false,
|
|
||||||
"encoding" : "UTF-8",
|
|
||||||
"folds" : "",
|
|
||||||
"hash" : "3423035371",
|
|
||||||
"id" : "EE21755B",
|
|
||||||
"lastKnownWriteTime" : 1423869219,
|
|
||||||
"path" : "~/Documents/GCAT4_old/trunk/R/GCAT/R/class.model.R",
|
|
||||||
"project_path" : "class.model.R",
|
|
||||||
"properties" : {
|
|
||||||
},
|
|
||||||
"source_on_save" : false,
|
|
||||||
"type" : "r_source"
|
|
||||||
}
|
|
||||||
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|||||||
{
|
|
||||||
}
|
|
||||||
@ -1,7 +0,0 @@
|
|||||||
~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2FGCAT.main.R="59ABD774"
|
|
||||||
~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2Fclass.model.R="6E6918EE"
|
|
||||||
~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2Ffit.model.R="5C623936"
|
|
||||||
~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2Ffitted.calculations.R="2ACDF6EF"
|
|
||||||
~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2Fnormalize.and.transform.R="F3CF638E"
|
|
||||||
~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2Fplot.fit.R="EFF3E540"
|
|
||||||
~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2Ftable2well.R="9402820B"
|
|
||||||
@ -1,35 +0,0 @@
|
|||||||
setwd("~/Downloads/")
|
|
||||||
file.list = file.name = "YPDAFEXglucoseTests_2-25-10.csv"
|
|
||||||
layout.file = "YPDAFEXglucoseTests_2-25-10_Layout.csv"
|
|
||||||
single.plate = T
|
|
||||||
out.dir = getwd()
|
|
||||||
graphic.dir = paste(out.dir, "/pics", sep = "")
|
|
||||||
add.constant = 1
|
|
||||||
blank.value = NULL
|
|
||||||
start.index = 2
|
|
||||||
growth.cutoff = 0.05
|
|
||||||
use.linear.param = F
|
|
||||||
use.loess = F
|
|
||||||
smooth.param = 0.6
|
|
||||||
points.to.remove = 0
|
|
||||||
remove.jumps = F
|
|
||||||
silent = F
|
|
||||||
verbose = T
|
|
||||||
return.fit = F
|
|
||||||
overview.jpgs = T
|
|
||||||
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")
|
|
||||||
|
|
||||||
t = gcat.analysis.main(file.list, single.plate, layout.file = NULL,
|
|
||||||
out.dir = getwd(), graphic.dir = paste(out.dir, "/pics", sep = ""),
|
|
||||||
add.constant = 1, blank.value = NULL, start.index = 2, growth.cutoff = 0.05,
|
|
||||||
use.linear.param=use.linear.param, use.loess=use.loess, smooth.param=0.1,
|
|
||||||
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 = F, verbose = F, return.fit = F, overview.jpgs = T)
|
|
||||||
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|
@ -0,0 +1,42 @@
|
|||||||
|
% Generated by roxygen2 (4.1.1): do not edit by hand
|
||||||
|
% Please edit documentation in R/slope.analysis.R
|
||||||
|
\name{check.slopes}
|
||||||
|
\alias{check.slopes}
|
||||||
|
\title{Use slope estimates to check growth curves for tanking and OD jumps #}
|
||||||
|
\usage{
|
||||||
|
check.slopes(input.well, check.start = 22, fall.cutoff = -0.0025,
|
||||||
|
remove.jumps = F, jump.multipliers = -c(15, 500, 10), tank.cutoff = 1,
|
||||||
|
tank.limit = 6, silent = T, draw = T)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{input.well}{object of class \code{well} to check the slopes for}
|
||||||
|
|
||||||
|
\item{check.start}{which timepoint should checking for jumps and tanking start at? this is included because early timepoints can be unstable.}
|
||||||
|
|
||||||
|
\item{fall.cutoff}{what downward slope should constitute a fall in OD?}
|
||||||
|
|
||||||
|
\item{remove.jumps}{should the program remove OD jumps? default F (just report them) -
|
||||||
|
should be set to T if data contains distinct jumps in OD that need to be eliminated
|
||||||
|
otherwise, this might be too stringent and will result in loss of data.}
|
||||||
|
|
||||||
|
\item{jump.multipliers}{multipliers of fall.cutoff that determine whether a curve jumps up or down (see methods 1 and 2, below)}
|
||||||
|
|
||||||
|
\item{tank.cutoff}{what proportion of the maximum OD can the curve go below until it is considered tanking?}
|
||||||
|
|
||||||
|
\item{tank.limit}{how many timepoints in a row can have falling slopes until the curve is marked as tanking?}
|
||||||
|
|
||||||
|
\item{silent}{output to R console?}
|
||||||
|
|
||||||
|
\item{draw}{plot growth curve with curve checking details?}
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Use slope estimates to check growth curves for tanking and OD jumps #
|
||||||
|
}
|
||||||
|
\details{
|
||||||
|
Uses the functions <data.from> and <well.name> (see well.class.R)
|
||||||
|
|
||||||
|
Fills the "curve.par" slot in the well with the starting index of tanking (NA if none is found)
|
||||||
|
|
||||||
|
Changed default values to parameters to account for settling
|
||||||
|
}
|
||||||
|
|
||||||
@ -0,0 +1,29 @@
|
|||||||
|
% Generated by roxygen2 (4.1.1): do not edit by hand
|
||||||
|
% Please edit documentation in R/plot.fit.R
|
||||||
|
\name{create.heatmap}
|
||||||
|
\alias{create.heatmap}
|
||||||
|
\title{Create a heat map of a plate}
|
||||||
|
\usage{
|
||||||
|
create.heatmap(fitted.well.array, attribute, MinMax = NA, unlog = NULL)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{fitted.well.array}{matrix containing well array object data}
|
||||||
|
|
||||||
|
\item{attribute}{the data type we should use to create a heatmap}
|
||||||
|
|
||||||
|
\item{MinMax}{The specific range for the heatmap.}
|
||||||
|
|
||||||
|
\item{unlog}{transform values to linear scale}
|
||||||
|
}
|
||||||
|
\value{
|
||||||
|
path of heatmap pdf file
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Create a heat map of a plate
|
||||||
|
}
|
||||||
|
\details{
|
||||||
|
This function is used to create a heatmap using
|
||||||
|
specific growth, total growth, or lag time
|
||||||
|
for each well on a plate.
|
||||||
|
}
|
||||||
|
|
||||||
@ -0,0 +1,17 @@
|
|||||||
|
% Generated by roxygen2 (4.1.1): do not edit by hand
|
||||||
|
% Please edit documentation in R/fit.model.R
|
||||||
|
\name{fit.nls.model}
|
||||||
|
\alias{fit.nls.model}
|
||||||
|
\title{Fit nls model to a well using a specified model}
|
||||||
|
\usage{
|
||||||
|
fit.nls.model(input.well, model)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{input.well}{object of class well}
|
||||||
|
|
||||||
|
\item{model}{object of class model, e.g. richards, gompertz or logistic}
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Fit nls model to a well using a specified model
|
||||||
|
}
|
||||||
|
|
||||||
@ -1,30 +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}
|
\name{GCAT}
|
||||||
\alias{GCAT}
|
\alias{GCAT}
|
||||||
\title{
|
\alias{GCAT-package}
|
||||||
Growth Curve Analysis Tool
|
\title{GCAT: Growth Curve Analysis Tool}
|
||||||
}
|
|
||||||
\description{
|
\description{
|
||||||
Mathematical modeling and parameter estimation of high volume microbial growth data.
|
Mathematical modeling and parameter estimation of high volume microbial growth data.
|
||||||
}
|
}
|
||||||
\details{
|
\details{
|
||||||
GCAT utilizes the \code{\link{nls}} function in the R base package to fit logistic and Richards models to
|
GCAT input is in .csv format. GCAT analysis is accessed using \code{\link{gcat.analysis.main}}
|
||||||
growth curve data. Input is in .csv format and analysis is accessed using \code{\link{gcat.analysis.main}}
|
|
||||||
or \code{\link{gcat.fit.main}}. Output is in .txt and .pdf format, and is accessed using \code{\link{gcat.analysis.main}}
|
|
||||||
or \code{\link{gcat.output.main}}.
|
|
||||||
|
|
||||||
\tabular{ll}{
|
GCAT utilizes the \code{\link[stats]{nls}} function in the R stats package to fit logistic, Gompertz and Richards models to growth curve
|
||||||
Version: \tab 5.0\cr
|
data. Best model is selected automatically. Alternatively, the user may choose LOESS local regression fits, implemented using
|
||||||
Depends: \tab pheatmap, gplots\cr
|
\code{\link[stats]{loess}} function in the R stats package
|
||||||
License: \tab LGPL-3\cr
|
|
||||||
Date: \tab 2014-02-10\cr
|
|
||||||
}
|
|
||||||
|
|
||||||
|
Internally, the data are stored in an array of \linkS4class{well} objects
|
||||||
}
|
}
|
||||||
\author{
|
|
||||||
Jason Shao\cr
|
|
||||||
Nate DiPiazza\cr
|
|
||||||
Yury Bukhman\cr
|
|
||||||
Minh Bui\cr
|
|
||||||
|
|
||||||
Maintainer: Yury Bukhman
|
|
||||||
}
|
|
||||||
@ -0,0 +1,15 @@
|
|||||||
|
% Generated by roxygen2 (4.1.1): do not edit by hand
|
||||||
|
% Please edit documentation in R/table2well.R
|
||||||
|
\name{gcat.append.arrays}
|
||||||
|
\alias{gcat.append.arrays}
|
||||||
|
\title{Function to combine two well array datasets by plate}
|
||||||
|
\usage{
|
||||||
|
gcat.append.arrays(...)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{...}{any number of array objects as long as they are all output straight from <load.data>}
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
This function can append together arrays created using <load.data>
|
||||||
|
}
|
||||||
|
|
||||||
@ -1,53 +0,0 @@
|
|||||||
\name{gcat.set.constants}
|
|
||||||
\alias{gcat.set.constants}
|
|
||||||
\title{
|
|
||||||
Set global constants for GCAT analysis package
|
|
||||||
}
|
|
||||||
\description{
|
|
||||||
Sets global constants, mostly regarding issues in input file format, for GCAT analysis.
|
|
||||||
}
|
|
||||||
\usage{
|
|
||||||
gcat.set.constants(plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0, time.format = "\%Y-\%m-\%d \%H:\%M:\%S",
|
|
||||||
multi.column.headers = c("Plate ID", "Well", "OD", "Time"), single.column.headers = c("", "A1"),
|
|
||||||
xlsx.data.headers = c("Plate ID", "Well positions"), xlsx.layout.sheet = "Plate layout",
|
|
||||||
layout.sheet.headers = c("Strain", "Media Definition"))
|
|
||||||
}
|
|
||||||
\arguments{
|
|
||||||
\item{plate.nrow}{
|
|
||||||
Number of rows present in each plate of input data. Default 8 (A-H)
|
|
||||||
}
|
|
||||||
\item{plate.ncol}{
|
|
||||||
Number of columns present in each plate of input data. Default 12 (1-12)
|
|
||||||
}
|
|
||||||
\item{input.skip.lines}{
|
|
||||||
Number of lines to skip at the top when reading input data files.
|
|
||||||
}
|
|
||||||
\item{time.format}{
|
|
||||||
Either a character describing the format used to convert timestamps
|
|
||||||
in the input to numbers representing number of seconds (see \code{\link{strptime}}), or a
|
|
||||||
factor to divide entries in the \code{Time} column by to get the number of hours.
|
|
||||||
}
|
|
||||||
\item{multi.column.headers}{
|
|
||||||
A character vector describing the names of the columns for
|
|
||||||
Plate ID, Well ID, Cellular density measurements and Time, respectively, in the multi-plate (long) format.
|
|
||||||
}
|
|
||||||
\item{single.column.headers}{
|
|
||||||
A character vector describing the name of the Time column and the first well data in the single plate (wide) format.
|
|
||||||
}
|
|
||||||
\item{xlsx.data.headers}{
|
|
||||||
For .xlsx data only, a vector describing possible entries in the upper left cell marking worksheets in each
|
|
||||||
workbook as containing data. .csv files don't have multiple worksheets and are assumed to contain useable data.
|
|
||||||
}
|
|
||||||
\item{xlsx.layout.sheet}{
|
|
||||||
For .xlsx data only, the name of the worksheet containing plate layout information. .csv files use a separate layout file.
|
|
||||||
}
|
|
||||||
\item{layout.sheet.headers}{
|
|
||||||
A character vector describing the name of the Strain and Media definiton columns, respectively, in the plate layout file.
|
|
||||||
}
|
|
||||||
}
|
|
||||||
\value{
|
|
||||||
NULL
|
|
||||||
}
|
|
||||||
\author{
|
|
||||||
Jason Shao
|
|
||||||
}
|
|
||||||
@ -0,0 +1,25 @@
|
|||||||
|
% Generated by roxygen2 (4.1.1): do not edit by hand
|
||||||
|
% Please edit documentation in R/table2well.R
|
||||||
|
\name{gcat.start.times}
|
||||||
|
\alias{gcat.start.times}
|
||||||
|
\title{Convert timestamps to hours from start and sort timepoints
|
||||||
|
This function acts on a single well and modifies the raw data stored in slot "screen.data"}
|
||||||
|
\usage{
|
||||||
|
gcat.start.times(input.well, time.input, start.index = 2)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{input.well}{an object of class well}
|
||||||
|
|
||||||
|
\item{time.input}{specifies time format in the input. allowed values are "%S", for seconds, "%d", for days, or anything complying with
|
||||||
|
ISO C / POSIX standards; see <strptime>.}
|
||||||
|
|
||||||
|
\item{start.index}{which timepoint should be used as the starting time at inoculation?}
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Convert timestamps to hours from start and sort timepoints
|
||||||
|
This function acts on a single well and modifies the raw data stored in slot "screen.data"
|
||||||
|
}
|
||||||
|
\details{
|
||||||
|
note: reading directly from excel to R results in timestamps being converted to days.
|
||||||
|
}
|
||||||
|
|
||||||
@ -0,0 +1,16 @@
|
|||||||
|
% Generated by roxygen2 (4.1.1): do not edit by hand
|
||||||
|
% Please edit documentation in R/class.well.R
|
||||||
|
\docType{methods}
|
||||||
|
\name{length,well-method}
|
||||||
|
\alias{length,well-method}
|
||||||
|
\title{Get the number of data points in a well}
|
||||||
|
\usage{
|
||||||
|
\S4method{length}{well}(x)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{x}{object of class \code{well}}
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Get the number of data points in a well
|
||||||
|
}
|
||||||
|
|
||||||
@ -0,0 +1,43 @@
|
|||||||
|
% Generated by roxygen2 (4.1.1): do not edit by hand
|
||||||
|
% Please edit documentation in R/normalize.and.transform.R
|
||||||
|
\name{normalize.ODs}
|
||||||
|
\alias{normalize.ODs}
|
||||||
|
\title{Normalize OD readings for an entire array of well objects}
|
||||||
|
\usage{
|
||||||
|
normalize.ODs(well.array, normalize.method = "default", blank.value = NULL,
|
||||||
|
start.index = 2, add.constant = 1)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{well.array}{an array of well objects.}
|
||||||
|
|
||||||
|
\item{normalize.method}{see Details}
|
||||||
|
|
||||||
|
\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{start.index}{which timepoint should be used as the first one after inoculation (defaults to the 2th one)}
|
||||||
|
|
||||||
|
\item{add.constant}{add a numeric constant to all timepoints in all wells.}
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Normalize OD readings for an entire array of well objects
|
||||||
|
}
|
||||||
|
\details{
|
||||||
|
Note: This function does not write any new OD values to the well objects in the array - it only
|
||||||
|
fills the "norm" slot of each well object in the array with a value that will be subtracted
|
||||||
|
from all OD measurements when returning data from the wells using the function <data.from> (see well.class.R)
|
||||||
|
|
||||||
|
These functions make use of <raw.data> which simply returns the raw time and OD of a well (also see well.class.R)
|
||||||
|
|
||||||
|
note this is the only normalization function that acts on an entire array instead of an individual well.
|
||||||
|
|
||||||
|
normalize.method settings:
|
||||||
|
\describe{
|
||||||
|
\item{default}{subtracts the blank OD (either specified by <blank.value> or taken from the first timepoint as default)
|
||||||
|
of each well from all timepoints in that well}
|
||||||
|
\item{average.blank}{subtracts the mean of all first OD timepoints on a plate from all timepoints in all wells on that plate}
|
||||||
|
\item{average.first}{takes the mean of the difference between the OD of the specified <start> timepoint and the first timepoint of all wells on a plate
|
||||||
|
and subtracts this value from all timepoints in all wells on that plate}
|
||||||
|
\item{anything else}{do nothing}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
@ -0,0 +1,43 @@
|
|||||||
|
% Generated by roxygen2 (4.1.1): do not edit by hand
|
||||||
|
% Please edit documentation in R/class.well.R
|
||||||
|
\docType{methods}
|
||||||
|
\name{plot,well,missing-method}
|
||||||
|
\alias{plot,well,missing-method}
|
||||||
|
\title{A plot method for well}
|
||||||
|
\usage{
|
||||||
|
\S4method{plot}{well,missing}(x, y, constant.added = 1, xlim = NULL,
|
||||||
|
ylim = NULL, well.number = NULL, scale = 1, number.points = T,
|
||||||
|
draw.symbols = F, show.text = T, show.calc = T, draw.guess = NULL,
|
||||||
|
...)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{x}{object of class well}
|
||||||
|
|
||||||
|
\item{y}{not used}
|
||||||
|
|
||||||
|
\item{constant.added}{used to readjust for the constant added during the log transform: log.OD = log(OD - blank + constant.added)}
|
||||||
|
|
||||||
|
\item{xlim}{x axis limits, vector of length 2}
|
||||||
|
|
||||||
|
\item{ylim}{y axis limits, vector of length 2}
|
||||||
|
|
||||||
|
\item{well.number}{the number of the well in an array of wells}
|
||||||
|
|
||||||
|
\item{scale}{determines the font scale for the entire graph. all cex values are calculated from this}
|
||||||
|
|
||||||
|
\item{number.points}{should points be labeled with numeric indices?}
|
||||||
|
|
||||||
|
\item{draw.symbols}{should <check.slopes> be called on the well and markings drawn on the graph?}
|
||||||
|
|
||||||
|
\item{show.text}{show R^2 and growth curve parameters as text on the plot}
|
||||||
|
|
||||||
|
\item{show.calc}{draw lines that illustrate growth curve parameters}
|
||||||
|
|
||||||
|
\item{draw.guess}{initial guess model. Drawn if specified}
|
||||||
|
|
||||||
|
\item{...}{additional arguments passed to the generic plot function}
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
A plot method for well
|
||||||
|
}
|
||||||
|
|
||||||
@ -0,0 +1,29 @@
|
|||||||
|
% Generated by roxygen2 (4.1.1): do not edit by hand
|
||||||
|
% Please edit documentation in R/table.output.R
|
||||||
|
\name{table.out}
|
||||||
|
\alias{table.out}
|
||||||
|
\title{Populate an output table with parameters and other useful info for each well in a fitted dataset.}
|
||||||
|
\usage{
|
||||||
|
table.out(fitted.data.set, unlog = F, constant.added, reach.cutoff = 0.9,
|
||||||
|
filename.timestamp = NULL, use.linear.param = F, use.loess = F)
|
||||||
|
}
|
||||||
|
\arguments{
|
||||||
|
\item{fitted.data.set}{array of fitted well objects}
|
||||||
|
|
||||||
|
\item{unlog}{- Should OD values be returned on the linear scale instead of log-transformed scale?}
|
||||||
|
|
||||||
|
\item{constant.added}{- For returning values on linear scale, what constant was added to ODs before the log transform?}
|
||||||
|
|
||||||
|
\item{reach.cutoff}{- what proportion of the plateau OD must tbe reached by the last valid timepoint for the curve to be marked as reaching
|
||||||
|
its plateau OD?}
|
||||||
|
|
||||||
|
\item{filename.timestamp}{timestamp for addition to output file names (for file references in last column of the output)}
|
||||||
|
|
||||||
|
\item{use.linear.param}{did the model formula contain a linear parameter? Should normally be FALSE, as the linear parameter is deprecated}
|
||||||
|
|
||||||
|
\item{use.loess}{was LOESS used to fit the data (instead of unsing a growth curve model formula)?}
|
||||||
|
}
|
||||||
|
\description{
|
||||||
|
Populate an output table with parameters and other useful info for each well in a fitted dataset.
|
||||||
|
}
|
||||||
|
|
||||||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in new issue