GCAT5.0 released

Testing/gcat_paper_code/explore_gcat_results_72h.R

@@ -0,0 +1,27 @@
+#  Explore GCAT results file for the 72h time course with 2 strains
+
+WORK.DIR = "/mnt/file.glbrc.org/ybukhman/Projects/GCAT_B05/GCAT 4/2_Piotrowski_data_analysis/working_data/GCAT_4.3_results/72h 128 vs 3d/loess_0.01"
+GCAT.FILE = "output_gcat.fit_2014-09-24_17.16.31.txt"
+
+#### Load data ####
+setwd(WORK.DIR)
+data1  = read.delim(GCAT.FILE,nrows=96)
+
+#### Assign strain id ####
+strain = rep("Lab",96)
+strain[grep("[ABCD]",data1$well)] = "Y128"
+
+#### Summarize fits of the lab strain ####
+summary(data1[strain=="Lab",])
+
+#  Why is reach so low?
+summary(data1$reach[strain=="Lab"])
+
+#### Compute CV of key parameters ####
+cv = function(x) {sd(x,na.rm=T)/mean(x,na.rm=T)}
+
+if ("shape.par" %in% names(data1)) {
+  apply(data1[strain=="Lab",c("lag.time","spec.growth","tot.growth","shape.par")],2,cv)
+} else {
+  apply(data1[strain=="Lab",c("lag.time","spec.growth","tot.growth")],2,cv)  
+}