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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
(specific growth rate, maximum growth capacity, and lag time)
for each well in a read.
Version: 6.0.1
Version: 6.0.2
Depends: pheatmap, gplots, methods
Maintainer: Yury Bukhman <ybukhman@glbrc.wisc.edu>
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 return.fit Whether should a fit well object is returned or not.
#' @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.
#'
#' @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 = ""),
add.constant = 0, blank.value, start.index, growth.cutoff = 0.05,
use.linear.param = F, use.loess = F, smooth.param=0.1,
lagRange = NA, totalRange = NA, specRange = NA,
lagRange = NA, totalRange = NA, totalODRange = NA, specRange = NA,
points.to.remove = 0, remove.jumps = F, time.input = NA,
plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,
multi.column.headers = c("Plate.ID", "Well", "OD", "Time"), single.column.headers = c("","A1"),
@ -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,
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,
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,
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)
@ -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 lagRange The heatmap specific range for lag time.
#' @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 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,
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,
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){
# 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,
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")
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 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 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
#'
create.heatmap = function(fitted.well.array, attribute, MinMax = NA, unlog=NULL){
create.heatmap = function(fitted.well.array, attribute, MinMax = NA, constant.added){
# debug
#browser()
@ -312,13 +313,14 @@ create.heatmap = function(fitted.well.array, attribute, MinMax = NA, unlog=NULL)
if(class(fitted.well.array) == "matrix"){
#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]
if(is.null(unlog)) {
spec.growth = unlist(aapply(fitted.well.array, attribute))
}
# currently only total growth needs to be unlogged if unlog == T
else {
if (attr.name == "achieved.growth.OD") {
# Need to pass constant.added to the attribute computation function
spec.growth = unlist(aapply(fitted.well.array, attribute, constant.added = constant.added))
} else {
# The attribute computation function does not have a constant.added argument
spec.growth = unlist(aapply(fitted.well.array, attribute))
}
num.dig = 3 #how many digits should be put on pdf?
max = round(max(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
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,
lagRange = NA, specRange = NA, totalRange = NA, ...){
lagRange = NA, specRange = NA, totalRange = NA, totalODRange = NA, ...){
# Prepare timestamp for addition to output file names.
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){
#Heatmap block##########################################################
#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")
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")
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")
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
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="")

20
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.
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"
# Run GCAT
library(GCAT)
setwd(INPUT.DIR)
time.input=1/3600
out = gcat.analysis.main(file.list = INPUT.FILE, single.plate = T, layout.file = NULL,
out.dir = OUTPUT.DIR, graphic.dir = OUTPUT.DIR,
# - do not specify parameter ranges
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,
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,
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}
\title{Create a heat map of a plate}
\usage{
create.heatmap(fitted.well.array, attribute, MinMax = NA, unlog = NULL)
create.heatmap(fitted.well.array, attribute, MinMax = NA, constant.added)
}
\arguments{
\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{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{
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 = ""),
add.constant = 0, blank.value, start.index, growth.cutoff = 0.05,
use.linear.param = F, use.loess = F, smooth.param = 0.1,
lagRange = NA, totalRange = NA, specRange = NA, points.to.remove = 0,
remove.jumps = F, time.input = NA, plate.nrow = 8, plate.ncol = 12,
input.skip.lines = 0, multi.column.headers = c("Plate.ID", "Well", "OD",
"Time"), single.column.headers = c("", "A1"),
layout.sheet.headers = c("Strain", "Media Definition"), silent = T,
verbose = F, return.fit = F, overview.jpgs = T)
lagRange = NA, totalRange = NA, totalODRange = NA, specRange = NA,
points.to.remove = 0, remove.jumps = F, time.input = NA,
plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,
multi.column.headers = c("Plate.ID", "Well", "OD", "Time"),
single.column.headers = c("", "A1"), layout.sheet.headers = c("Strain",
"Media Definition"), silent = T, verbose = F, return.fit = F,
overview.jpgs = T)
}
\arguments{
\item{file.list}{A list of full paths to .csv files. all files must be in the same format (see <single.plate>)}
@ -42,7 +43,9 @@ gcat.analysis.main(file.list, single.plate, layout.file = NULL,
\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.}

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(),
graphic.dir = paste(out.dir, "/pics", sep = ""), overview.jpgs = T,
use.linear.param = F, use.loess = F, lagRange = NA, totalRange = NA,
specRange = NA, plate.nrow = 8, plate.ncol = 12, unlog = F,
silent = T, main.envir)
totalODRange = NA, specRange = NA, plate.nrow = 8, plate.ncol = 12,
unlog = F, silent = T, main.envir)
}
\arguments{
\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{totalODRange}{The heatmap specific range for the achieved growth on linear (OD) scale.}
\item{specRange}{The heatmap specific range for spec growth rate.}
\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
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,
: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
@ -169,6 +169,10 @@ class Assay
self.totg_min = Float(self.totg_min)
self.totg_max = Float(self.totg_max)
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 != '')
self.lagT_max = Float(self.lagT_max)
self.lagT_min = Float(self.lagT_min)
@ -351,6 +355,13 @@ class Assay
else
R.eval 'totalRange <- NA'
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 != '')
R.assign 'lagT_min', self.lagT_min
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)
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,
totalRange = totalRange, specRange = specRange, points.to.remove = points.to.remove, remove.jumps, time.input, plate.nrow = 8,
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,
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"),
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>
</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">
<%= 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.label "-" %>
<%= f.text_field(:totg_max, :type => 'number', :min => '1', :size => '2') %>
</div>
<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.label "-" %>
<%= f.text_field(:specg_max, :type => 'number', :min => '1', :size => '2') %>

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