User:James Estevez/Notebook/Spring 2011: Bdellovibrio Independent Study/2011/02/21

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Generating figures in R

Not exactly intuitive, but it's coming along. Location is indicated by a number:

1 Cytoplasmic
2 Cytoplasmic Membrane
3 Periplasmic
4 Outer Membrane
5 Extracellular
6 Unknown



Hexagon Binning

I didn't like how these came out so I tried the hexbin package from BioConductor

Source code

# Clear all variables and plots
rm(list = ls())       
graphics.off()       
 
# Import localization data
bd100_numloc_asc<-read.csv('/home/james/Data/bdcost/R/N/bd100_psortb_asc_numloc.csv')
bm_numloc_asc<-read.csv('/home/james/Data/bdcost/R/N/b_marinus_psort_ASC_numloc.csv')
 
library(RSvgDevice)  # Output to SVG for direct manipulation in Inkscape  
devSVG(file='scatter_asc.svg', height=6, width=12, onefile=TRUE) # Height and width are in inches
 
par(mfcol = c(1,2))
 
# Plot vs location
plot(bm_numloc_asc$asc,jitter(bm_numloc_asc$F_L_num), 
	main="Average Synthetic Cost (ASC)", 
	sub="B. marinus SJ", 
	xlab = "ATPs/aa", 
	ylab = "Location",
	pch=".")
plot(bd100_numloc_asc$asc,jitter(bd100_numloc_asc$F_L_num), 
	sub="B. bacteriovorax ", 
	xlab = "ATPs/aa", 
	ylab = "Location",
	pch=".")
title(main="Average Synthetic Cost (ASC)")
dev.off()
 
 
# These don't look right, so let's try hexbinned plots of the same data
library(hexbin)
hplot_bm <- hexbin(bm_numloc_asc$asc,jitter(bm_numloc_asc$F_L_num))
hplot_bd100 <- hexbin(bd100_numloc_asc$asc,jitter(bd100_numloc_asc$F_L_num))
 
devSVG(file='hex_asc_bm.svg', height=6, width=9, onefile=TRUE) # SVG output
 
plot(hplot_bm,	
	main="Average Synthetic Cost (ASC) in B. marinus SJ", 
	xlab = "ATPs/aa", 
	ylab = "Location")
dev.off()
devSVG(file='hex_asc_bd100.svg', height=6, width=9, onefile=TRUE) 
plot(hplot_bd100,		
	main = "Average Synthetic Cost (ASC) in B. bacteriovorax HD100", 
	xlab = "ATPs/aa", 
	ylab = "Location")
dev.off()


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