Session Two

General Information

There are 18 GMT modules that directly create (or add overlays to) plots; the remaining 45 are mostly concerned with data processing. This session will focus on the task of plotting lines, symbols, and text on maps. We will build on the skills we acquired while familiarizing ourselves with the various GMT map projections as well as how to select a data domain and boundary annotations.

Program	Purpose
BASEMAPS
basemap	Create an empty basemap frame with optional scale
coast	Plot coastlines, filled continents, rivers, and political borders
legend	Create legend overlay
POINTS AND LINES
wiggle	Draw spatial time-series along their (x,y)-tracks
plot	Plot symbols, polygons, and lines in 2-D
plot3d	Plot symbols, polygons, and lines in 3-D
HISTOGRAMS
histogram	Plot a rectangular histogram
rose	Plot a polar histogram(sector/rose diagram)
CONTOURS
grdcontour	Contouring of grids
contour	Direct contouring/imaging of (x,y,z) data by optimal triangulation
SURFACES
grdimage	Project and plot grids or images
grdvector	Plot vector fields from grids
grdview	3-D perspective imaging of grids
UTILITIES
clip	Use polygon files to initiate custom clipping paths
image	Plot Sun raster files
mask	Create clipping paths or generate overlay to mask
colorbar	Plot gray scale or color scale bar
text	Plot text strings

Plotting lines and symbols, plot is one of the most frequently used modules in GMT. In addition to the common command line switches it has numerous specific options, and expects different file formats depending on what action has been selected. These circumstances make plot harder to master than most GMT tools. The table below shows an abbreviated list of the options:

Option	Purpose
steps	Suppress line interpolation along great circles
cmap=cpt	Let symbol color be determined from z-values and the cpt file
error_bars=(x|y|X|Y=true, wiskers=true, cap=width, pen=pen,	Draw selected error bars with specified attributes
colored=true, cline=true, csymbol=true)
fill=fill	Set color for symbol or fill for polygons
close[options]	Explicitly close polygons or create polygon
no_clip=true [no_clip=:c|no_clip=:r]	Do Not clip symbols at map borders
symbol=(symb=name, size=val, unit=unity)	Select one of several symbols
pen=pen	Set pen for line or symbol outline

The symbols can either be transparent (using pen only, not fill) or solid (fill, with optional outline using pen). The symbol or marker option takes the code for the desired symbol and optional size information. If no symbol is given it is expected to be given in the last column of each record in the input file. The size is optional since individual sizes for symbols may also be provided by the input data. The main symbols available to us are shown in the table below:

Option	Symbol
marker=”-”	horizontal dash; size is length of dash
marker=:star	star; size is radius of circumscribing circle
marker=:bar	bar; size is bar width, set unit be u if size is in x-units
	Bar extends from base [0] to the y-value
marker=:circle	circle; size is the diameter
marker=:d	diamond; size is its side
marker=:ellipse	ellipse; direction (CCW from horizontal), major, and minor axes
	are read from the input file
marker=:Ellipse	Ellipse; azimuth (CW from vertical), major, and minor axes in kilometers
	are read from the input file
marker=:octagon	octagon; size is its side
marker=:hexagon	hexagon; size is its side
marker=:inverted_tri	inverted triangle; size is its side
marker=”kustom/size”	kustom symbol; size is its side
marker=:pentagon	pentagon; size is its side
marker=:point	point; no size needed (1 pixel at current resolution is used)
marker=:rectangle	rect, width and height are read from input file
marker=:square	square, size is its side
marker=:triangle	triangle; size is its side
marker=:vector params	vector; direction (CCW from horizontal) and length are read from input data
	Append parameters of the vector; see plot for syntax.
marker=:Vector params	Vector, except azimuth (degrees east of north) is expected instead of direction
	The angle on the map is calculated based on the chosen map projection
marker=:wedge	pie wedge; start and stop directions (CCW from horizontal) are read from input
marker=:cross	cross; size is length of crossing lines
marker=”y-dash”	vertical dash; size is length of dash

The symbol option in plot. Lower case symbols (a, c, d, g, h, i, n, s, t, x) will fit inside a circle of given diameter. Upper case symbols (A, C, D, G, H, I, N, S, T, X) will have area equal to that of a circle of given diameter.

Because some symbols require more input data than others, and because the size of symbols as well as their color can be determined from the input data, the format of data can be confusing. The general format for the input data is (optional items are in brackets []):

x y [ z ] [ size ] [ sigma_x ] [ sigma_y ] [ symbol ]

Thus, the only required input columns are the first two which must contain the longitude and latitude (or x and y). The remaining items apply when one (or more) of the following conditions are met:

1. If you want the color of each symbol to be determined individually, supply a CPT with the cmap option and let the 3rd data column contain the z-values to be used with the CPT.

2. If you want the size of each symbol to be determined individually, append the size in a separate column.

3. To draw error bars, use the error_bars option and give one or two additional data columns with the dx and dy values; the form of error_bars determines if one (error_bars=(x=true,) and/or error_bars=(y=true,)) columns are needed. If wiskers=true is given then we will instead draw a “box-and-whisker” symbol and the sigma_x (or sigma_y) must represent 4 columns containing the minimum, the 25 and 75% quartiles, and the maximum value. The given x (or y) coordinate is taken as the 50% quantile (median).

4. If you draw vectors with marker=vector then size is actually two columns containing the direction and length of each vector.

5. If you draw ellipses (marker=ellipse) then size is actually three columns containing the direction and the major and minor axes in plot units (with marker=Ellipse we expect azimuth instead and axes lengths in km).

Before we try some examples we need to review two key switches; they specify pen attributes and symbol or polygon fill. Please consult the General Features section the GMT Technical Reference and Cookbook before experimenting with the examples below.

Examples:

We will start off using the file tut_data.txt in your directory. Using the GMT utility gmtinfo we find the extent of the data region:

gmtinfo("@tut_data.txt")

which returns

tut_data.txt: N = 7   <1/5>   <1/5>

telling us that the file tut_data.txt has 7 records and gives the minimum and maximum values for the first two columns. Given our knowledge of how to set up linear projections with region and proj=:linear, try the following:

1. Plot the data as transparent circles of size 0.75 centimeters.

2. Plot the data as solid white circles instead.

3. Plot the data using 0.5” stars, making them red with a thick (width = 1.5p), dashed pen.

To simply plot the data as a line we choose no symbol and specify a pen thickness instead:

plot("@tut_data.txt", region=(0,6,0,6), pen=:thinner, aspect=:equal, show=true)

Your plot should look like our example 7 below

Result of GMT Tutorial example 7

Exercises:

1. Plot the data as a green-blue polygon instead.

2. Try using a predefined pattern.

A common question is : “How can I plot symbols connected by a line with plot?”. The surprising answer is that we must call plot twice. While this sounds cumbersome there is a reason for this: Basically, polygons need to be kept in memory since they may need to be clipped, hence computer memory places a limit on how large polygons we may plot. Symbols, on the other hand, can be plotted one at the time so there is no limit to how many symbols one may plot. Therefore, to connect symbols with a line we must use the overlay approach:

plot("@tut_data.txt", region=(0,6,0,6), pen=:thinner, marker=:inverted_tri,
     markersize=0.5, aspect=:equal, show=true)

Your plot should look like our example 8 below. The two-step procedure also makes it easy to plot the line over the symbols instead of symbols over the line, as here.

Result of GMT Tutorial example 8

Our final plot example involves a more complicated scenario in which we want to plot the epicenters of several earthquakes over the background of a coastline basemap. We want the symbols to have a size that reflects the magnitude of the earthquakes, and that their color should reflect the depth of the hypocenter. The first few lines in the remote tut_quakes.ngdc looks like this:

Historical Tsunami Earthquakes from the NCEI Database
Year  Mo  Da  Lat+N  Long+E  Dep  Mag
1987  01  04  49.77  149.29  489  4.1
1987  01  09  39.90  141.68  067  6.8

Thus the file has three header records (including the blank line), but we are only interested in columns 5, 4, 6, and 7. In addition to extract those columns we must also scale the magnitudes into symbols sizes in centimeters. Given their range it looks like multiplying the magnitude by 0.1 will work well for symbol sizes in cm. Reformatting this file to comply with the plot input format can be done in a number of ways. Here, we simply use the common column selection option incol and its scaling/offset capabilities. To skip the first 3 header records and then select the 4th, 3rd, 5th, and 6th column and scale the last column by 0.1, we would use

incols="4,3,5,6s0.1", header=3

(Remember that 0 is the first column). We will follow conventional color schemes for seismicity and assign red to shallow quakes (depth 0-100 km), green to intermediate quakes (100-300 km), and blue to deep earthquakes (depth > 300 km). The quakes.cpt file establishes the relationship between depth and color:

# color palette for seismicity
#z0  color   z1 color
0    red    100 red
100  green  300 green
300  blue  1000 blue

Apart from comment lines (starting with #), each record in the CPT governs the color of a symbol whose z value falls in the range between z_0 and z_1. If the colors for the lower and upper levels differ then an intermediate color will be linearly interpolated given the z value. Here, we have chosen constant color intervals. You may wish to consult the Color palette tables section in the Cookbook. This color table was generated as part of the script (below).

We may now complete our example using the Mercator projection:

C = makecpt(cmap="red,green,blue", range="0,100,300,10000");
coast(region=(130,150,35,50), land=:gray, proj=:merc)
plot!("@tut_quakes.ngdc", incols="4,3,5,6s0.1", header=3, symbol="cc", markerline=:faint, color=C, show=true)

where the second c used in the symbol option ensures that symbols sizes are interpreted to be in cm. Your plot should look like our example 9 below

Result of GMT Tutorial example 9

More exercises

1. Select another symbol.

2. Let the deep earthquakes be cyan instead of blue.

Plotting text strings

In many situations we need to annotate plots or maps with text strings; in GMT this is done using text. Apart from the common switches, there are 8 options that are particularly useful.

Option	Purpose
clearance=(margin=(dx,dy),)	Spacing between text and the text box (see pen)
offset=([away=true, corners=true,] shift=(dx,dy) [,line=pen])	Offsets the projected location of the strings
attribparams	Set font, justify, angle values or source
fill=_fill_	Fills the text bos using specified fill
list=true	Lists the font ids and exits
noclip=true	Deactivates clipping at the borders
shade=true	Plot a shadow behind the text box.
pen=pen	Draw the outline of text box

The input data to text is expected to contain the following information:

[ x   y ]  [ font]  [ angle ] [ justify ]   my text

The font is the optional font to use, the angle is the angle (measured counterclockwise) between the text’s baseline and the horizontal, justify indicates which anchor point on the text-string should correspond to the given x, y location, and my text is the text string or sentence to plot. See the Technical reference for the relevant two-character codes used for justification.

The text string can be one or several words and may include octal codes for special characters and escape-sequences used to select subscripts or symbol fonts. The escape sequences that are recognized by GMT are given below:

Code	Effect
@~	Turns symbol font on or off
@+	Turns superscript on or off
@-	Turns subscript on or off
@#	Turns small caps on or off
@_	Turns underline on or off
@%font%	Switches to another font; @%% resets to previous font
@:size:	Switches to another font size; @:: resets to previous size
@;color;	Switches to another font color; @;; resets to previous color
@!	Creates one composite character of the next two characters
@@	Prints the @ sign itself

Note that these escape sequences (as well as octal codes) can be used anywhere in GMT, including in arguments to the frame option. A chart of octal codes can be found in Appendix F in the GMT Technical Reference. For accented European characters you must set PS_CHAR_ENCODING to ISOLatin1 in your gmt.conf file.

We will demonstrate text with the following script:

T = text_record(
   1  1  It's P@al, not Pal!
   1  2  Try @%33%ZapfChancery@%% today
   1  3  @~D@~g@-b@- = 2@~pr@~G@~D@~h.
   1  4  University of Hawaii at M@!a\225noa
);
text(T, region=(0,7,0,5), font=(30, "Times-Roman", :DarkOrange), jutify=:BL)

Your plot should look like our example 10 below

Result of GMT Tutorial example 10

Code	Effect	Code	Effect
@E	Æ	@e	æ
@O	Ø	@o	ø
@A	Å	@a	å
@C	Ç	@c	ç
@N	Ñ	@n	ñ
@U	Ü	@u	ü
@s	ß

Exercises:

1. At y = 5, add the sentence \(z^2 = x^2 + y^2\).

2. At y = 6, add the sentence “It is 32° today”.