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33 lines
1.9 KiB
33 lines
1.9 KiB
# Test that heatmaps are processed and generated correctly
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# Yury V Bukhman, 01 July 2015
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# This script generates heat maps with pre-set limits. Manually check output directory to see if they make sense.
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INPUT.DIR = system.file("extdata/YPDAFEXglucoseTests_2-25-10",package="GCAT")
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OUTPUT.DIR.1 = paste(system.file("extdata/heatmap_tests",package="GCAT"),"temp1",sep="/")
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OUTPUT.DIR.2 = paste(system.file("extdata/heatmap_tests",package="GCAT"),"temp2",sep="/")
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INPUT.FILE = "YPDAFEXglucoseTests_2-25-10.csv"
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# Run GCAT
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library(GCAT)
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setwd(INPUT.DIR)
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time.input=1/3600
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# - do specify parameter ranges
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out2 = gcat.analysis.main(file.list = INPUT.FILE, single.plate = T, layout.file = NULL,
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out.dir = OUTPUT.DIR.2, graphic.dir = OUTPUT.DIR.2,
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add.constant = 1, blank.value = NULL, start.index = 2, growth.cutoff = 0.05,
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use.linear.param=F, use.loess=F, smooth.param=0.1,
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points.to.remove = integer(), remove.jumps = F, time.input=time.input,
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silent = F, verbose = T, return.fit = T, overview.jpgs = T,
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lagRange = c(0,3), totalRange = c(0.2,0.82), totalODRange = c(0.06,1), specRange = c(0.04,0.13))
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# - do not specify parameter ranges
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out1 = gcat.analysis.main(file.list = INPUT.FILE, single.plate = T, layout.file = NULL,
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out.dir = OUTPUT.DIR.1, graphic.dir = OUTPUT.DIR.1,
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add.constant = 1, blank.value = NULL, start.index = 2, growth.cutoff = 0.05,
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use.linear.param=F, use.loess=F, smooth.param=0.1,
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points.to.remove = integer(), remove.jumps = F, time.input=time.input,
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silent = F, verbose = T, return.fit = T, overview.jpgs = T)
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# Verify that specifying parameter ranges did not affect any computations except for how the heat maps are drawn
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all.equal(out1,out2) |