Useful graphical devices.R

# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# This script presents a simple example of plotting using several graphical devices
# For a list of graphical devices offered in R just run ?Devices

# Note that journals usually accept PDF as vector format and TIFF for images
# PDF is the easiest way to use when it comes to creating graphs in vector format.
# Also the EPS (postscript) format is widely accepted by journals.
# For TIFF files, use the "LZW compression" option when saving. 
# That will significantly reduce the file size, without adversely affecting the image quality
# (http://esapubs.org/esapubs/preparation.htm#Ill).
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

# create some random example data
x <- rnorm(5000)
y <- rnorm(5000)

# ==================================================================================
# A)    Simple plotting of scatterplot (no device)
# ==================================================================================
plot(x,y, main = "", 
     col = rgb(red = 0, green = 0, blue = 0, alpha = 0.15), 
     pch = 16)
# col = rgb() - creates RGB colors and alpha gives color transparency

# ==================================================================================
# B)    Plotting scatterplot with PDF graphics device driver
# ==================================================================================
# This is the most practical way I often use. PDF files can be imported in Inkscape 
# (https://inkscape.org/en/, is open source) and then can be 
# saved to a multitude of formats.
# 
# open the graphic device with desired parameters
pdf(file = "Scatterplot as PDF (10 by 9 cm).pdf",
    width = 10/2.54, height = 9/2.54, 
    family = "Times", pointsize = 8)
# Since "width" and "height" need to be in inches, one can still use cm 
# and divide by 2.54 to make the conversion to inch.
# family="Times" refers to the font family (here: Times New Roman).
# Check this link for some family fonts: http://www.statmethods.net/advgraphs/parameters.html
# pointsize = 8 refers to the point size used, here (Times New Roman) 8

# plot the scatterplot
plot(x,y, main = "", 
     col = rgb(red = 0, green = 0, blue = 0, alpha = 50, maxColorValue = 255), 
     pch = 16)
# col = rgb() - creates RGB colors and alpha gives color transparency
# check ?rgb for further help

# close the device
dev.off()

# ==================================================================================
# C)    Plotting scatterplot with enhanced metafile (EMF) graphics device driver
# ==================================================================================
# 'EMF' can be imported as vector graphics in both OpenOffice and Microsoft Office

# NOTE: The EMF format does not allow for color transparency.
# Attempting to use a transparent color will result in a warning message
# (from: https://cran.r-project.org/web/packages/devEMF/devEMF.pdf)
# Solution - plot as PDF, then import in Inkscape (https://inkscape.org/en/, is open source) 
# and then export to a multitude of formats, EMF included.

# library "devEMF" is required
if (!require("devEMF")) {
        install.packages("devEMF")
        library("devEMF")
}

# open the graphic device with desired parameters
emf(file = "Scatterplot as EMF (10 by 9 cm).emf", 
    width = 10/2.54, height = 9/2.54,
    family = "Times", pointsize = 8)
# Since "width" and "height" need to be in inches, one can still use cm 
# and divide by 2.54 to make the conversion to inch.
# family="Times" refers to the font family (here: Times New Roman).
# pointsize = 8 refers to the point size used, here (Times New Roman) 8

# plot the scatterplot
plot(x,y, main = "", 
     col = rgb(red = 0, green = 0, blue = 0, maxColorValue = 255), 
     pch = 16)
# col = rgb() - creates RGB colors
# check ?rgb for further help

# close the device
dev.off()

# ==================================================================================
# D)    Plotting scatterplot with postscript graphics device driver
# ==================================================================================
# NOTE: The postscript format does not allow for color transparency.
# For alternatives check 'cairo_ps' function from the grDevices package
# (http://stackoverflow.com/questions/4001316/how-do-i-preserve-transparency-in-ggplot2)
# Or plot as PDF, then import in Inkscape (https://inkscape.org/en/, is open source) 
# and then export to a multitude of formats (e.g. SVG or EPS)

# open the graphic device with desired parameters
postscript(file = "Scatterplot as postscript (10 by 9 cm).ps",
           width = 10/2.54, height = 9/2.54, 
           family = "Times", pointsize = 8)
# Since "width" and "height" need to be in inches, one can still use cm 
# and divide by 2.54 to make the conversion to inch.
# family="Times" refers to the font family (here: Times New Roman).
# pointsize = 8 refers to the point size used, here (Times New Roman) 8

# plot the scatterplot
plot(x,y, main = "", 
     col = rgb(red = 0, green = 0, blue = 0, maxColorValue = 255), 
     pch = 16)
# col = rgb() - creates RGB colors
# check ?rgb for further help

# close the device
dev.off()

# ==================================================================================
# E)    Plotting scatterplot with TIFF graphics device drive
# ==================================================================================
# For TIFF files, use the "LZW compression" option when saving the files. 
# That will significantly reduce the file size, without adversely affecting the image quality
# (http://esapubs.org/esapubs/preparation.htm#Ill).

# open the graphic device with desired parameters
tiff(file = "Scatterplot as tiff (10 by 9 cm).tif",
     width = 10, height = 9, units = "cm", res = 600,
     family = "Times", pointsize = 8, 
     compression = "lzw", type = "cairo")
# units = "cm" specifies the units for width and height
# res = 600 - the nominal resolution in ppi
# family = "Times" refers to the font family (here: Times New Roman).
# pointsize = 8 refers to the point size used, here (Times New Roman) 8
# compression = "lzw" reduces the file size, without adversely affecting the image quality 
# (advice from http://esapubs.org/esapubs/preparation.htm#Ill)
# type = "cairo" - plotting using cairographics; https://en.wikipedia.org/wiki/Cairo_(graphics)

# plot the scatterplot
plot(x,y, main = "", 
     col = rgb(red = 0, green = 0, blue = 0, alpha = 50, maxColorValue = 255), 
     pch = 16)
# col = rgb() - creates RGB colors and alpha gives color transparency
# check ?rgb for further help

# close the device
dev.off()