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46 lines
1.9 KiB
46 lines
1.9 KiB
10 years ago
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# Explore strain collection results:
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# 1) Variety of sigmoid models
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# 2) Correlation between sigmoid and loess
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WORK.DIR = "/mnt/file.glbrc.org/ybukhman/Projects/GCAT_B05/B05.06 GCAT paper/2014 Bioenergy Research/Supplementary data/4 strains in 12 media/GCAT_outputs"
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SIGMOID.FILE = "sigmoid/output_gcat.fit_2014-10-03_16.40.42.txt"
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LOESS.FILE = "loess_0.1/output_gcat.fit_2014-10-03_16.44.11.txt"
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EMPTY.WELLS = c(paste(LETTERS[1:8],rep(c("01","06","11","12"),each=8),sep=""),
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paste(rep(c("A0","H0"),each=7),rep(c(2:5,7:9),2),sep=""),
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"A10","H10",
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paste("B0",2:5,sep=""))
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#WORK.DIR = "/mnt/file.glbrc.org/ybukhman/Projects/GCAT_B05/GCAT 4/2_Piotrowski_data_analysis/working_data/GCAT_4.3_results/ACSH686 GWASv1"
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#SIGMOID.FILE = "sigmoid/output_gcat.fit_2014-09-25_09.43.27.txt"
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#LOESS.FILE = "loess_0.1/output_gcat.fit_2014-09-25_09.45.57.txt"
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#EMPTY.WELLS = c(paste(LETTERS[2:7],"01",sep=""),
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# paste(rep(c("A0","H0"),each=9),rep(c(1:9),2),sep=""),
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# paste(rep(c("A","H"),each=3),rep(10:12,2),sep=""),
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# "B12","G12")
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# Load data
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setwd(WORK.DIR)
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sigmoid = read.delim(SIGMOID.FILE,nrows=96)
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loess = read.delim(LOESS.FILE,nrows=96)
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# Filter out empty wells
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sigmoid = subset(sigmoid, ! well %in% EMPTY.WELLS)
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loess = subset(loess, ! well %in% EMPTY.WELLS)
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# Summarize sigmoid models
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summary(sigmoid$model)
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# Correlation between growth curve parameters computed using sigmoid and loess models
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cor(sigmoid$lag.time,loess$lag.time)
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cor(sigmoid$spec.growth,loess$spec.growth)
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cor(sigmoid$tot.growth,loess$tot.growth)
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plot.corr = function(loess,sigmoid,param,title) {
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plot(loess[,param],sigmoid[,param],xlab="loess",ylab="sigmoid",main=title)
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abline(0,1)
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}
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plot.corr(loess,sigmoid,"lag.time","Lag Time")
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plot.corr(loess,sigmoid,"spec.growth","Specific Growth Rate")
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plot.corr(loess,sigmoid,"tot.growth","Total Growth")
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