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Added support for heat maps of achieved growth on linear scale. Still having trouble with the input form in Rails.

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pull/3/head
Yury V Bukhman 9 years ago
parent 745f8a70af
commit 105be75c26
9 changed files with 82 additions and 39 deletions
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2
R/GCAT/DESCRIPTION
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@ -8,7 +8,7 @@ Description: Imports high-throughput growth curve data from microtiter
GCAT estimates important growth characteristics GCAT estimates important growth characteristics
(specific growth rate, maximum growth capacity, and lag time) (specific growth rate, maximum growth capacity, and lag time)
for each well in a read. for each well in a read.
Version: 6.0.1 Version: 6.0.2
Depends: pheatmap, gplots, methods Depends: pheatmap, gplots, methods
Maintainer: Yury Bukhman <ybukhman@glbrc.wisc.edu> Maintainer: Yury Bukhman <ybukhman@glbrc.wisc.edu>
License: LGPL-3 License: LGPL-3

12
R/GCAT/R/GCAT.main.R
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@ -107,7 +107,8 @@ global.version.number = packageDescription(pkg="GCAT")$Version
#' @param overview.jpgs Should GCAT enable an overview image? #' @param overview.jpgs Should GCAT enable an overview image?
#' @param return.fit Whether should a fit well object is returned or not. #' @param return.fit Whether should a fit well object is returned or not.
#' @param lagRange The heatmap specific range for lag time. #' @param lagRange The heatmap specific range for lag time.
#' @param totalRange The heatmap specific range for the achieved growth. #' @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 specRange The heatmap specific range for spec growth rate. #' @param specRange The heatmap specific range for spec growth rate.
#' #'
#' @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
@ -117,7 +118,7 @@ gcat.analysis.main = function(file.list, single.plate, layout.file = NULL,
out.dir = getwd(), graphic.dir = paste(out.dir, "/pics", sep = ""), out.dir = getwd(), graphic.dir = paste(out.dir, "/pics", sep = ""),
add.constant = 0, blank.value, start.index, 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, use.linear.param = F, use.loess = F, smooth.param=0.1,
lagRange = NA, totalRange = 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, 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"),
@ -184,7 +185,7 @@ gcat.analysis.main = function(file.list, single.plate, layout.file = NULL,
source.file.list = source.file.list, upload.timestamp = upload.timestamp, source.file.list = source.file.list, upload.timestamp = upload.timestamp,
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, lagRange = lagRange, specRange = specRange, totalRange = totalRange, totalODRange = totalODRange,
out.dir = out.dir, graphic.dir = graphic.dir, overview.jpgs=overview.jpgs, 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)
@ -480,6 +481,7 @@ gcat.fit.main = function(file.name, input.data = NULL, load.type = "csv", layout
#' @param plate.ncol The number of columns for a plate #' @param plate.ncol The number of columns for a plate
#' @param lagRange The heatmap specific range for lag time. #' @param lagRange The heatmap specific range for lag time.
#' @param totalRange The heatmap specific range for the achieved growth. #' @param totalRange The heatmap specific range for the achieved growth.
#' @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
#' #'
@ -487,7 +489,7 @@ gcat.fit.main = function(file.name, input.data = NULL, load.type = "csv", layout
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,
use.linear.param=F, use.loess=F, lagRange = NA, totalRange = 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){
# Prepare timestamp for addition to output file names. # Prepare timestamp for addition to output file names.
@ -558,7 +560,7 @@ 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,
plate.ncol = plate.ncol, plate.nrow = plate.nrow),silent=silent) totalODRange = totalODRange, 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)

29
R/GCAT/R/plot.fit.R
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@ -298,12 +298,13 @@ plot_residuals = function(input.well, xlim = NULL, lowess = T, ...){
#' #'
#' @param fitted.well.array matrix containing well array object data #' @param fitted.well.array matrix containing well array object data
#' @param attribute the data type we should use to create a heatmap #' @param attribute the data type we should use to create a heatmap
#' @param unlog transform values to linear scale
#' @param MinMax The specific range for the heatmap. #' @param MinMax The specific range for the heatmap.
#' @param constant.added the numeric constant that was added to each curve before the log transform:
#' same as \code{add.constant} in \link{gcat.analysis.main}
#' #'
#' @return path of heatmap pdf file #' @return path of heatmap pdf file
#' #'
create.heatmap = function(fitted.well.array, attribute, MinMax = NA, unlog=NULL){ create.heatmap = function(fitted.well.array, attribute, MinMax = NA, constant.added){
# debug # debug
#browser() #browser()
@ -312,13 +313,14 @@ create.heatmap = function(fitted.well.array, attribute, MinMax = NA, unlog=NULL)
if(class(fitted.well.array) == "matrix"){ if(class(fitted.well.array) == "matrix"){
#We may want to sub() out periods from plate.ID if it causes problems #We may want to sub() out periods from plate.ID if it causes problems
plate.ID = unique(unlist(aapply(fitted.well.array,plate.name)))[1] plate.ID = unique(unlist(aapply(fitted.well.array,plate.name)))[1]
if(is.null(unlog)) { if (attr.name == "achieved.growth.OD") {
spec.growth = unlist(aapply(fitted.well.array, attribute)) # Need to pass constant.added to the attribute computation function
} spec.growth = unlist(aapply(fitted.well.array, attribute, constant.added = constant.added))
# currently only total growth needs to be unlogged if unlog == T } else {
else { # The attribute computation function does not have a constant.added argument
spec.growth = unlist(aapply(fitted.well.array, attribute)) spec.growth = unlist(aapply(fitted.well.array, attribute))
} }
num.dig = 3 #how many digits should be put on pdf? num.dig = 3 #how many digits should be put on pdf?
max = round(max(spec.growth, na.rm=T), digits=num.dig) max = round(max(spec.growth, na.rm=T), digits=num.dig)
min = round(min(spec.growth, na.rm=T), digits=num.dig) min = round(min(spec.growth, na.rm=T), digits=num.dig)
@ -614,7 +616,7 @@ 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, ...){ lagRange = NA, specRange = NA, totalRange = NA, totalODRange = NA, ...){
# 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")
@ -645,17 +647,20 @@ pdf.by.plate = function(fitted.data, out.prefix = "", upload.timestamp = NULL,
if(num.wells > 1){ if(num.wells > 1){
#Heatmap block########################################################## #Heatmap block##########################################################
#alongside the jpgs file create 3 heatmaps for each plate. NWD #alongside the jpgs file create 3 heatmaps for each plate. NWD
spec.heat.file = create.heatmap(fitted.data[,,i], max.spec.growth.rate, MinMax = specRange) spec.heat.file = create.heatmap(fitted.data[,,i], max.spec.growth.rate, MinMax = specRange, constant.added)
if(spec.heat.file == "Error") if(spec.heat.file == "Error")
stop("Error in <create.heatmap> for specific growth") stop("Error in <create.heatmap> for specific growth")
lag.heat.file = create.heatmap(fitted.data[,,i], lag.time, MinMax = lagRange) lag.heat.file = create.heatmap(fitted.data[,,i], lag.time, MinMax = lagRange, constant.added)
if(lag.heat.file == "Error") if(lag.heat.file == "Error")
stop("Error in <create.heatmap> for lag time") stop("Error in <create.heatmap> for lag time")
total.heat.file = create.heatmap(fitted.data[,,i], achieved.growth, MinMax = totalRange) total.heat.file = create.heatmap(fitted.data[,,i], achieved.growth, MinMax = totalRange, constant.added)
if(total.heat.file == "Error") if(total.heat.file == "Error")
stop("Error in <create.heatmap> for total growth") stop("Error in <create.heatmap> for total growth")
total.OD.heat.file = create.heatmap(fitted.data[,,i], achieved.growth.OD, MinMax = totalODRange, constant.added)
if(total.OD.heat.file == "Error")
stop("Error in <create.heatmap> for total growth")
# Add name of file if successfully written to file list output. Including heatmap files NWD # Add name of file if successfully written to file list output. Including heatmap files NWD
file.list.out = c(file.list.out, spec.heat.file, lag.heat.file, total.heat.file) file.list.out = c(file.list.out, spec.heat.file, lag.heat.file, total.heat.file, total.OD.heat.file)
######################################################################## ########################################################################
} }
jpg.name = paste(out.dir, "/", plate.ID, "_overview", ".jpg", sep="") jpg.name = paste(out.dir, "/", plate.ID, "_overview", ".jpg", sep="")

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R/GCAT/inst/extdata/heatmap_tests/test_heatmap_limits.R vendored
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@ -3,18 +3,30 @@
# This script generates heat maps with pre-set limits. Manually check output directory to see if they make sense. # This script generates heat maps with pre-set limits. Manually check output directory to see if they make sense.
INPUT.DIR = system.file("extdata/YPDAFEXglucoseTests_2-25-10",package="GCAT") INPUT.DIR = system.file("extdata/YPDAFEXglucoseTests_2-25-10",package="GCAT")
OUTPUT.DIR = paste(system.file("extdata/heatmap_tests",package="GCAT"),"temp",sep="/") OUTPUT.DIR.1 = paste(system.file("extdata/heatmap_tests",package="GCAT"),"temp1",sep="/")
OUTPUT.DIR.2 = paste(system.file("extdata/heatmap_tests",package="GCAT"),"temp2",sep="/")
INPUT.FILE = "YPDAFEXglucoseTests_2-25-10.csv" INPUT.FILE = "YPDAFEXglucoseTests_2-25-10.csv"
# Run GCAT # Run GCAT
library(GCAT) library(GCAT)
setwd(INPUT.DIR) setwd(INPUT.DIR)
time.input=1/3600 time.input=1/3600
out = gcat.analysis.main(file.list = INPUT.FILE, single.plate = T, layout.file = NULL, # - do not specify parameter ranges
out.dir = OUTPUT.DIR, graphic.dir = OUTPUT.DIR, out1 = gcat.analysis.main(file.list = INPUT.FILE, single.plate = T, layout.file = NULL,
out.dir = OUTPUT.DIR.1, graphic.dir = OUTPUT.DIR.1,
add.constant = 1, blank.value = NULL, start.index = 2, growth.cutoff = 0.05,
use.linear.param=F, use.loess=F, smooth.param=0.1,
points.to.remove = integer(), remove.jumps = F, time.input=time.input,
silent = F, verbose = T, return.fit = T, overview.jpgs = T)
# - do specify parameter ranges
out2 = gcat.analysis.main(file.list = INPUT.FILE, single.plate = T, layout.file = NULL,
out.dir = OUTPUT.DIR.2, graphic.dir = OUTPUT.DIR.2,
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,
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,
lagRange = c(0,3), totalRange = c(0.2,0.82), specRange = c(0.04,0.13)) lagRange = c(0,3), totalRange = c(0.2,0.82), totalODRange = c(0.06,1), specRange = c(0.04,0.13))
# Verify that specifying parameter ranges did not affect any computations except for how the heat maps are drawn
all.equal(out1,out2)

5
R/GCAT/man/create.heatmap.Rd
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@ -4,7 +4,7 @@
\alias{create.heatmap} \alias{create.heatmap}
\title{Create a heat map of a plate} \title{Create a heat map of a plate}
\usage{ \usage{
create.heatmap(fitted.well.array, attribute, MinMax = NA, unlog = NULL) create.heatmap(fitted.well.array, attribute, MinMax = NA, constant.added)
} }
\arguments{ \arguments{
\item{fitted.well.array}{matrix containing well array object data} \item{fitted.well.array}{matrix containing well array object data}
@ -13,7 +13,8 @@ create.heatmap(fitted.well.array, attribute, MinMax = NA, unlog = NULL)
\item{MinMax}{The specific range for the heatmap.} \item{MinMax}{The specific range for the heatmap.}
\item{unlog}{transform values to linear scale} \item{constant.added}{the numeric constant that was added to each curve before the log transform:
same as \code{add.constant} in \link{gcat.analysis.main}}
} }
\value{ \value{
path of heatmap pdf file path of heatmap pdf file

17
R/GCAT/man/gcat.analysis.main.Rd
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@ -8,12 +8,13 @@ gcat.analysis.main(file.list, single.plate, layout.file = NULL,
out.dir = getwd(), graphic.dir = paste(out.dir, "/pics", sep = ""), out.dir = getwd(), graphic.dir = paste(out.dir, "/pics", sep = ""),
add.constant = 0, blank.value, start.index, 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, use.linear.param = F, use.loess = F, smooth.param = 0.1,
lagRange = NA, totalRange = NA, specRange = NA, points.to.remove = 0, lagRange = NA, totalRange = NA, totalODRange = NA, specRange = NA,
remove.jumps = F, time.input = NA, plate.nrow = 8, plate.ncol = 12, points.to.remove = 0, remove.jumps = F, time.input = NA,
input.skip.lines = 0, multi.column.headers = c("Plate.ID", "Well", "OD", plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,
"Time"), single.column.headers = c("", "A1"), multi.column.headers = c("Plate.ID", "Well", "OD", "Time"),
layout.sheet.headers = c("Strain", "Media Definition"), silent = T, single.column.headers = c("", "A1"), layout.sheet.headers = c("Strain",
verbose = F, return.fit = F, overview.jpgs = T) "Media Definition"), silent = T, verbose = F, return.fit = F,
overview.jpgs = T)
} }
\arguments{ \arguments{
\item{file.list}{A list of full paths to .csv files. all files must be in the same format (see <single.plate>)} \item{file.list}{A list of full paths to .csv files. all files must be in the same format (see <single.plate>)}
@ -42,7 +43,9 @@ gcat.analysis.main(file.list, single.plate, layout.file = NULL,
\item{lagRange}{The heatmap specific range for lag time.} \item{lagRange}{The heatmap specific range for lag time.}
\item{totalRange}{The heatmap specific range for the achieved growth.} \item{totalRange}{The heatmap specific range for the achieved growth on log scale.}
\item{totalODRange}{The heatmap specific range for the achieved growth on linear (OD) scale.}
\item{specRange}{The heatmap specific range for spec growth rate.} \item{specRange}{The heatmap specific range for spec growth rate.}

6
R/GCAT/man/gcat.output.main.Rd
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@ -9,8 +9,8 @@ gcat.output.main(fitted.well.array, out.prefix = "", source.file.list,
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, use.linear.param = F, use.loess = F, lagRange = NA, totalRange = NA,
specRange = NA, plate.nrow = 8, plate.ncol = 12, unlog = F, totalODRange = NA, specRange = NA, plate.nrow = 8, plate.ncol = 12,
silent = T, main.envir) 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.}
@ -50,6 +50,8 @@ This is for backwards compatibility with the old web server.}
\item{totalRange}{The heatmap specific range for the achieved growth.} \item{totalRange}{The heatmap specific range for the achieved growth.}
\item{totalODRange}{The heatmap specific range for the achieved growth on linear (OD) scale.}
\item{specRange}{The heatmap specific range for spec growth rate.} \item{specRange}{The heatmap specific range for spec growth rate.}
\item{plate.nrow}{The number of rows for a plate.} \item{plate.nrow}{The number of rows for a plate.}

18
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, :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
# (1) Validation of input data file # (1) Validation of input data file
@ -169,6 +169,10 @@ class Assay
self.totg_min = Float(self.totg_min) self.totg_min = Float(self.totg_min)
self.totg_max = Float(self.totg_max) self.totg_max = Float(self.totg_max)
end end
if (self.totg_OD_min != '' && self.totg_OD_max != '')
self.totg_OD_min = Float(self.totg_OD_min)
self.totg_OD_max = Float(self.totg_OD_max)
end
if (self.lagT_min != '' && self.lagT_max != '') if (self.lagT_min != '' && self.lagT_max != '')
self.lagT_max = Float(self.lagT_max) self.lagT_max = Float(self.lagT_max)
self.lagT_min = Float(self.lagT_min) self.lagT_min = Float(self.lagT_min)
@ -351,6 +355,13 @@ class Assay
else else
R.eval 'totalRange <- NA' R.eval 'totalRange <- NA'
end end
if (self.totg_OD_min != '' && self.totg_OD_max != '')
R.assign 'totODMin', self.totg_OD_min
R.assign 'totODMax', self.totg_OD_max
R.eval "totalODRange <- c(totODMin, totODMax)"
else
R.eval 'totalODRange <- NA'
end
if (self.lagT_min != '' && self.lagT_max != '') if (self.lagT_min != '' && self.lagT_max != '')
R.assign 'lagT_min', self.lagT_min R.assign 'lagT_min', self.lagT_min
R.assign 'lagT_max', self.lagT_max R.assign 'lagT_max', self.lagT_max
@ -361,8 +372,9 @@ class Assay
# 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, lagRange = lagRange, start.index, growth.cutoff, use.linear.param=use.linear.param, use.loess=use.loess, smooth.param=smooth.param,
totalRange = totalRange, specRange = specRange, points.to.remove = points.to.remove, remove.jumps, time.input, plate.nrow = 8, lagRange = lagRange, totalRange = totalRange, totalODRange = totalODRange, specRange = specRange,
points.to.remove = points.to.remove, remove.jumps, time.input, plate.nrow = 8,
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)')

12
Rails/app/views/assays/_form.html.erb
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@ -128,15 +128,21 @@
</div> </div>
</li> </li>
<li> <li>
<h3><span data-tooltip="Select the range for the heatmaps for easier comparison.">Heatmap options</span></h3> <h3><span data-tooltip="Select value ranges for the heatmaps for easier comparison between experiments.">Heatmap options</span></h3>
<div class="field"> <div class="field">
<%= f.label "Enter the range for the total growth." %><br /> <%= f.label "Enter the range for the achieved growth on log scale." %><br />
<%= f.text_field(:totg_min, :type => 'number', :min => '0', :size => '2') %> <%= f.text_field(:totg_min, :type => 'number', :min => '0', :size => '2') %>
<%= f.label "-" %> <%= f.label "-" %>
<%= f.text_field(:totg_max, :type => 'number', :min => '1', :size => '2') %> <%= f.text_field(:totg_max, :type => 'number', :min => '1', :size => '2') %>
</div> </div>
<div class="field"> <div class="field">
<%= f.label "Enter the range for the specific growth." %><br /> <%= f.label "Enter the range for the achieved growth on linear scale." %><br />
<%= f.text_field(:totg_OD_min, :type => 'number', :min => '0', :size => '2') %>
<%= f.label "-" %>
<%= f.text_field(:totg_OD_max, :type => 'number', :min => '1', :size => '2') %>
</div>
<div class="field">
<%= f.label "Enter the range for the max specific growth rate." %><br />
<%= f.text_field(:specg_min, :type => 'number', :min => '0', :size => '2') %> <%= f.text_field(:specg_min, :type => 'number', :min => '0', :size => '2') %>
<%= f.label "-" %> <%= f.label "-" %>
<%= f.text_field(:specg_max, :type => 'number', :min => '1', :size => '2') %> <%= f.text_field(:specg_max, :type => 'number', :min => '1', :size => '2') %>

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