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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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Yury V Bukhman
2015-07-02 16:07:27 -05:00
parent 745f8a70af
commit 105be75c26
9 changed files with 82 additions and 39 deletions
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R/GCAT/inst/extdata/heatmap_tests/test_heatmap_limits.R
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+16 -4
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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)