#15 Alkali Silica Template


Alkali Silica

Does what it says on the tin.

DOWNLOAD THE CODE

#------------------------------
#-------- INFORMATION ---------
#------------------------------
# Plotting points from Hugh
# Rallinson's "Using Geochemical
# Data" book. Code compiled by
# Darren J. Wilkinson,
# Grant Inst. Earth Science
# The University of Edinburgh
# d.j.wilkinson@ed.ac.uk
#------------------------------

# -------- CONTROLS ----------
y.max = 16
x.min = 35
x.max = 80
lab.size = 5
save = "/Users/s0679701/Desktop/"
filename = "test.png"
#------------------------------

# -------- LIBRARIES ----------
library (grid)
library (scales)
library (ggplot2)
#------------------------------

# -------- DON'T EDIT ----------
a = c(1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 4, 4, 4, 5, 5, 5, 5, 6, 6, 6, 6, 7, 7, 7, 8, 8)
x = c(41.0,41.0,52.5,50.0,52.5,57.6,63.0,63.0,45.0,45.0,61.0,63.5,45.0,52.0,57.0,63.0,69.0,45.0,49.4,52.0,52.0, 48.4,53.0,57.0,57.0,69.0,69.0,76.6,41.0,45.0)
y = c(0.500,7.000,14.000,15.126,14.000,11.700,7.000,0.500,0.500,5.000,13.500,14.830,5.000,5.000,5.900, 7.000,8.000,9.400,7.300,5.000,0.500,11.500,9.300,5.900,0.500,12.500,8.000,0.500,3.000,3.000)
lines = data.frame (a, x, y)

b = c("Picro-Basalt", "Basalt", "Basaltic Andesite", "Andesite", "Dacite", "Basanite", "Trachy Basalt", "Basaltic Trachyandesite", "Trachyandesite", "Trachydacite", "Rhyolite", "Tephrite", "Phonotephrite", "Tephriphonolite", "Trachyte", "Foidite", "Phonolite")
c = c(1:17)
x = c(43, 48.5, 54.5, 60, 68, 43, 48.75, 53, 57.5, 65, 75, 46, 49, 53, 65, 45, 58)
y = c(2, 2.5, 3, 3.5, 4, 6, 5.5, 6.5, 8.5, 9, 8, 8, 9.5, 11.5, 12, 13, 14)
labels = data.frame (b, x, y)

x = c(39.8,65.5) #MacDonald (1968)
y = c(0.35, 9.7) #MacDonald (1968)
sub = data.frame (x, y)
#------------------------------

# -------- BEGIN PLOT ----------

ggplot (lines, aes (x=x, y=y)) +

# Field Boundaries
geom_line (
aes(linewidth = factor (a))
) +

# Alkaline-Tholeiitic Line
geom_line (
data = sub,
aes (x=x, y=y),
linetype = "longdash"
) +

# Field Labels
geom_text (
data = labels,
aes(x = x, y = y, label = b),
size = lab.size
) +

scale_x_continuous (
name = (expression(paste("SiO"["2"], " (wt. %)"))),
limits = c(x.min, x.max)
) +

scale_y_continuous (
name = (expression(paste("Na"["2"], "O + K"["2"], "O", " (wt. %)"))),
breaks = c(seq(0, y.max, 2)),
limits = c(0, y.max)
) +

theme (
plot.title = element_text (vjust = 3, size = 20), #plot title
plot.margin = unit (c(3, 3, 3, 3), "lines"), #adjust the margins of the entire plot
panel.border = element_rect (colour = "black", fill = F, size = 2), #change the colour of the axes to black
panel.grid.major = element_blank (), # remove major grid
panel.grid.minor = element_blank (), # remove minor grid
panel.background = element_rect (fill = "white"), #makes the background transparent (white) NEEDED FOR INSIDE TICKS
legend.background = element_rect (fill = "white"),
legend.justification=c(1, 1),
legend.position = c(1, 1), # put the legend INSIDE the plot area
legend.key = element_blank (), # switch off the rectangle around symbols in the legend
legend.title = element_blank (), # switch off the legend title
legend.text = element_text (size = 15), #sets the attributes of the legend text
axis.title.x = element_text (vjust = -2, size = 20), #change the axis title
axis.title.y = element_text (vjust = -0.1, angle = 90, size = 20), #change the axis title
axis.text.x = element_text (size = 17, vjust = -0.25, colour = "black"), #change the axis label font attributes
axis.text.y = element_text (size = 17, hjust = 1, colour = "black"), #change the axis label font attributes
axis.ticks = element_line (colour = "black", size = 0.5), #sets the thickness and colour of axis ticks
axis.ticks.length = unit(-0.25 , "cm"), #setting a negative length plots inside, but background must be FALSE colour
axis.ticks.margin = unit(0.5, "cm") # the margin between the ticks and the text
)

ggsave (paste (save, filename), height = 12, width = 18, dpi = 75)

#14 A New GGPLOT Template


Screen Shot 2013-02-13 at 10.46.11

 

So the opts() has now been given the boot, and all the cool kids are using theme() to customise their ggplots. If you’re still on an old version of R then theme() will still work, but if you update (which you should) then it’ll stop working and you’ll have to edit all your code which uses theme ().

Here is my standard template giving you a style for simple, publication friendly ggplot plots.

# Load Packages
library (ggplot2) # Needed for plotting
library (grid) # Needed for customising plot area
library (scales) # Needed for ediring log tickmarks

# Select Font Size
size1 = 20 # Plot and Axis Titles
size2 = 17 # Legend Title
size3 = 15 # Axis Labels

ggplot (
     data = mtcars,
     aes (
     x= disp,
     y= drat
     )
     ) +

geom_point (
     aes(
     colour = mpg
     ),
     size = 5
     ) +

scale_y_log10 (
     limits = c(0.01, 10),
     name = "Axis Title Here",
     label = trans_format('log10',math_format(10^.x)) # Format = 10^x rather than 1e10x (also use label = comma)
     ) +

scale_x_log10 (
      limits = c(10, 1000),
     name = "Axis Title Here",
     label = trans_format('log10',math_format(10^.x)) # Format = 10^x rather than 1e10x (also use label = comma)
     ) +

annotation_logticks ( # Turn on minor ticks
     short = unit (0.2, "cm"), # Minor tick length
     mid = unit (0.2, "cm"), # ...
     long = unit (0.2, "cm"), # ...
     side = "lbrt") + # l = left, b = bottom etc

labs ( # New way of setting some attributes.
     colour = "MPG",
     title = "Plot Title"
     ) +

theme (
      plot.title = element_text (vjust = 3, size = 20), # plot title attrib.
      plot.margin = unit (c(3, 3, 3, 3), "lines"), # plot margins
      panel.border = element_rect (colour = "black", fill = F, size = 1), # axis colour = black
      panel.grid.major = element_blank (), # remove major grid
      panel.grid.minor = element_blank (), # remove minor grid
      panel.background = element_rect (fill = "white"), # background colour
      legend.background = element_rect (fill = "white"), # background colour
      legend.justification=c(0, 0), # lock point for legend
      legend.position = c(0, 0), # put the legend INSIDE the plot area
      legend.key = element_blank (), # switch off the rectangle around symbols in the legend
      legend.title = element_blank (), # switch off the legend title
      legend.text = element_text (size = 15), # sets the attributes of the legend text
      axis.title.x = element_text (vjust = -2, size = 20), # change the axis title
      axis.title.y = element_text (vjust = -0.1, angle = 90, size = 20), # change the axis title
      axis.text.x = element_text (size = 17, vjust = -0.25, colour = "black"),# change the axis label font attributes
      axis.text.y = element_text (size = 17, hjust = 1, colour = "black"), # change the axis label font attributes
      axis.ticks = element_line (colour = "black", size = 0.5), # sets the thickness and colour of axis ticks
      axis.ticks.length = unit(-0.25 , "cm"), # -ve length = inside ticks
      axis.ticks.margin = unit(0.5, "cm") # margin between the ticks and the text
      )

#13 Mapping in R: Representing geospatial data together with ggplot


homies1

I have been trawling around for a while now trying to find a simple and understandable way of representing geospatial data in R, whilst retaining the ability to manipulate the visualisation in ggplot. After much searching I came across some articles which got me to a working product only after a lot of ball ache. All the coding is done in R, so if you don’t know what it is click here. I keep the code simple, mainly because I don’t need it to be more complex for my purposes, but it also helps newbies like me learn the syntax faster.

GGMAP is a package that was developed by David Kahle and Hadley Wickham (Hadley being the guy behind ggplot2). If you want more detail see David’s slides from the 8th International R User Conference.

 
1.0 Fetching a Map

Maps may be brought into R from a number of sources, the two main ones are GoogleMaps and OpenStreetMap. The code needed to fetch the map is slightly different depending on where you want the data from. Below are some examples:

 
libary (ggmap) 

ggmap(
	get_googlemap(
		center=c(-3.17486, 55.92284), #Long/lat of centre, or "Edinburgh"
		zoom=14, 
		maptype='satellite', #also hybrid/terrain/roadmap
		scale = 2), #resolution scaling, 1 (low) or 2 (high)
		size = c(600, 600), #size of the image to grab
		extent='device', #can also be "normal" etc
		darken = 0) #you can dim the map when plotting on top

ggsave ("/Users/s0679701/Desktop/map.png", dpi = 200) #this saves the output to a file

This outputs the following files:

maptype = "satellite"

maptype = “satellite”

maptype = "roadmap"

maptype = “roadmap”

maptype = "terrain"

maptype = “terrain”

We can also obtain a map from OpenStreetMap:

libary (ggmap) 

ggmap(
	get_openstreetmap (
	bbox = c(-3.16518, 55.91899, -3.18473, 55.92716), 
	format = "png"
	),

ggsave ("/Users/s0679701/Desktop/map.png", dpi = 200) #this saves the output to a file

You may receive the following error:

 Error: map grabbing failed - see details in ?get_openstreetmap.
In addition: Warning message:
In download.file(url, destfile = destfile, quiet = !messaging, mode = "wb") :
  cannot open: HTTP status was '503 Service Unavailable'

This is because the OpenMapServer has issues, and so you just need to be lucky! Hence why there is no OpenStreetMap for this example…. yet.

 
2.0 Plotting on a Map

You can plot any [x,y, +/- z] information you’d like on top of a ggmap, so long as x and y correspond to longitudes and latitudes within the bounds of the map you have fetched. To plot on top of the map you must first make your map a variable and add a geom layer to it. Here is an example:

libary (ggmap) 

#Generate some data
long = c(-3.17904, -3.17765, -3.17486, -3.17183)
lat = c(55.92432, 55.92353, 55.92284, 55.92174)
who = c("Darren", "Rachel", "Johannes", "Romesh")
data = data.frame (long, lat, who)

map = ggmap(
	get_googlemap(
		center=c(-3.17486, 55.92284), 
		zoom=16, 
		maptype='hybrid', 
		scale = 2), 

		size = c(600, 600),
		extent='normal', 
		darken = 0)

map + geom_point (
		data = data,
		aes (
			x = long, 
			y = lat, 
			fill = factor (who)
			), 
		pch = 21, 
		colour = "white", 
		size = 6
		) +

	scale_fill_brewer (palette = "Set1", name = "Homies") +

	#for more info on these type ?theme()	
	theme ( 
		legend.position = c(0.05, 0.05), # put the legend INSIDE the plot area
		legend.justification = c(0, 0),
		legend.background = element_rect(colour = F, fill = "white"),
		legend.key = element_rect (fill = F, colour = F),
		panel.grid.major = element_blank (), # remove major grid
		panel.grid.minor = element_blank (),  # remove minor grid
		axis.text = element_blank (), 
		axis.title = element_blank (),
		axis.ticks = element_blank ()
		) 

ggsave ("/Users/s0679701/Desktop/map.png", dpi = 200)

homies1homies2

This simple code should be enough to get you going making your own plots. If you have any questions about this code or your own, then please don’t hesitate with getting in touch via the comments below.

Happy Mapping!