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Tuesday, 5 May 2015

Export a high resolution graph for publication

Most journals require high resolution images for publication. Portland Press - publishers connected with the Biochemical Society - "require BLACK AND WHITE figures (e.g. line diagrams, bar graphs etc.) as .tiff files at 600 dots per inch (dpi) or .eps files at 600 dpi."

Below is the code to create a graph that is appropriate for publication. The tiff file is very large and will probable need some compression. 

Code: 
### START of SCRIPT
# Publication quality graphs require 600dpi
dpi=600    #pixels per square inch
tiff("output.tif", width=6*dpi, height=5*dpi, res=dpi)
# the tiff() function creates the output file
# and adds information about size and resolution 

# data
prot <- c(0.000, 0.016, 0.031, 0.063, 0.125, 0.250, 0.500, 1.000, 0.000, 0.016, 0.031, 0.063, 0.125, 0.250, 0.500, 1.000) 
abs <- c(0.329, 0.352, 0.349, 0.379, 0.417, 0.491, 0.668, 0.956, 0.327, 0.341, 0.355, 0.383, 0.417, 0.446, 0.655, 0.905)

#draw the graph:
plot(abs~prot, 
     xlab = "[Protein] (microg/ml)",
     ylab = "Absorbance (570nm)",
     main = "Protein Assay")
line <- lm(abs~prot) # Calculate the line
abline(line) # Draw the line

r2 <- round(summary(line)$r.squared, 3)
mylabel = bquote(italic(R)^2 == .(format(r2, digits = 3)))
text(x = 0.2, y = 0.9, labels = mylabel)

dev.off()  #very important command 
# tells R that you are finished plotting
# otherwise your graph will not show up.
## END OF SCRIPT


This script generates TIFF files but similar commands are also available for PNG files, PDFs, SVGs and others. 

Check your like the file.
Will also work with combined figures. 
With PDFs you can adjust in other packages like Adobe Illustrator. 

Here is a list of resources that give me some good tips and info:

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