11. Plotting

Plotting is straightforward:

$ cis plot variable:filenames

This will attempt to locate the variable variable in all of the specified filenames, work out its metadata, such as units, labels, etc. and the appropriate chart type to plot, so that a line graph is used for two dimensional data, a scatter plot is used for three dimensional ungridded data and a heatmap for three dimensional gridded data. Other types of chart can be specified using the --type option. Available types are:

a simple line plot, for three dimensional data the third variable is represented by the line colour
a scatter plot
a scatter plot with two coordinate axis and the data represented by the colour of the marker
a heatmap especially suitable for gridded data
a standard contour plot, see contour options
a filled contour plot, see contour options



allows two variables to be plotted against each other, specified as cis plot variable1:filename1 variable2:filename2 --type comparativescatter
a Taylor diagram for comparing collocated datasets. See Taylor, K. E. (2001), ‘Summarizing multiple aspects of model performance in a single diagram’, J. Geophys. Res., 106(D7), 7183–7192, doi:10.1029/2000JD900719 for a detailed description.

Note that filenames is a non-optional argument used to specify the files to read the variable from. These can be specified as a comma separated list of the following possibilities:

  1. A single filename - this should be the full path to the file
  2. A single directory - all files in this directory will be read
  3. A wildcarded filename - A filename with any wildcards compatible with the python module glob, so that *, ? and [] can all be used. For example /path/to/my/test*file_[0-9].

Note that when using option 2, the filenames in the directory will be automatically sorted into alphabetical order. When using option 3, the filenames matching the wildcard will also be sorted into alphabetical order. The order of the comma separated list will however remain as the user specified, e.g.:

$ cis plot $var:filename1,filename2,wildc*rd,/my/dir/,filename3

would read filename1, then filename2, then all the files that match wildc*rd (in alphabetical order), then all the files in the directory /my/dir/ (in alphabetical order) and then finally filename3.

11.1. Plot Options

There are a number of optional arguments, which should be entered as a comma separated list after the mandatory arguments, for example variable:filename:product=Cis,edgecolor=black. The options are:

colour of markers, e.g. for scatter plot points or contour lines, see Available Colours and Markers
colour map to use, e.g. for contour lines or heatmap, see Available Colours and Markers
the minimum value for the colourmap
the maximum value for the colourmap
colour of scatter marker edges (can be used to differentiate scatter markers with a colourmap from the background plot)
shape of scatter marker, see Available Colours and Markers
width of an item. Units are points in the case of a line, and points^2 in the case of a scatter point
name of datagroup for the legend
the data product to use for the plot
the type of plot for that layer. This can’t be set if the global type has been set.
the transparancy of that layer
The label for the colorbar
The orientation of the colour bar, either horizontal or vertical
Hides the colour bar on a 3D plot
this can be used to change the size of the colourbar when plotting and defaults to 0.55 for vertical colorbars, 1.0 for horizontal.

Additional datagroup options for contour plots only:

the number of levels for the contour plot
a list of levels for the contour plot, e.g. contlevels=[0,1,3,10]
options are true or false, if true then contour labels are shown
width of the contour lines

Note that label refers to the label the plot will have on the legend, for example if a multi-series line graph or scatter plot is plotted. To set the labels of the axes, use --xlabel and --ylabel. --cbarlabel can be used to set the label on the colour bar.

The axes can be specified with --xaxis and --yaxis. Gridded data supports any coordinate axes available in the file, while ungridded data supports the following coordinate options (if available in the data):

  • latitude
  • longitude
  • time
  • altitude
  • air_pressure
  • variable - the variable being plotted

If the product is not specified, the program will attempt to figure out which product should be used based on the filename. See What kind of data can CIS deal with? to see a list of available products and their file signatures, or run cis plot -h.

11.2. Saving to a File

By default a plot will be displayed on screen. To save it to an image file instead, use the --output option. Available output types are png, pdf, ps, eps and svg, which can be selected using the appropriate filename extension, for example --output plot.svg.

11.3. Plot Formatting

There are a number of plot formatting options available:

The label for the x axis
The label for the y axis
The title of the plot
The size of the font in points
The colour map to be used when plotting a 3D plot, see Available Colours and Markers
The projection to use for the map-plot. All Cartopy projections are supported, see http://scitools.org.uk/cartopy/docs/latest/crs/projections.html for a full list.
The height of the plot, in inches
The width of the plot, in inches
The number of bins on the x axis of a histogram
The number of bins on the y axis of a histogram
Shows grid lines
The colour of the coastlines on a map, see Available Colours and Markers
Use the NASA Blue Marble for the background, instead of coastlines, when doing lat-lon plots
Plot the bias between the data sets using specified mechanism. Can be either ‘color’, ‘colour’, ‘size’ or ‘flag’
Use solid markers
Extend plot for negative correlation
Fold plot for negative correlation or large variance
Fix maximum extent of radial axis
Fix maximum standardised bias

11.4. Setting Plot Ranges

The arguments --xmin, --xmax, --xstep, --ymin, --ymax, --ystep, --vmin, --vmax, --vstep can be used to specify the range of values to plot, where x and y correspond to the axes and v corresponds to the colours.

When the arguments refer to dates or times, they should be in the format YYYY-MM-DDThh:mm:ss, where the time is optional. A colon or a space is also a valid date and time separator (if using a space quotes are necessary).

The step arguments are used to specify the tick spacing on the axes and vstep is used to specify the tick spacing on the colorbar.

When the step arguments refer to an amount of time, they should be in the ISO 8601 format PnYnMnDTnHnMnS, where any particular time group is optional, case does not matter, and T can be substituted for either a colon or a space (if using a space quotes are necessary).

For example, to specify a tick spacing of one month and six seconds on the x axis, the following argument should be given: --xstep 1m6S

Note: If a value is negative, then an equals sign must be used, e.g. --xmin=-5.

To plot using a log scale:

The x axis will be plotted using a log scale of base 10
The y axis will be plotted using a log scale of base 10
The values (colours) will be plotted using a log scale of base 10

11.5. Overlaying Multiple Plots

Overlaying multiple plots is straightforward, simply use the plot command as before but specify multiple files and variables, e.g.:

$ cis plot $var1:$filename1:edgecolor=black $var2:$filename2:edgecolor=red

To plot two variables from the same file, simply use the above command with $filename1 in place of $filename2.

The type paramter can be used to specify different types for each layer. For example, to plot a heatmap and a contour plot the following options can be used:

cis plot var1:file1:type=heatmap var2:file2:type=contour,color=white --width 20 --height 15 --cbarscale 0.5 -o overlay.png

Note that the default plot dimensions are deduced from the first datagroup specified.

Many more examples are available in the overlay examples page.

11.6. Available Colours and Markers

CIS recognises any valid html colour, specified using its name e.g. red for options such as item colour (line/scatter colour) and the colour of the coast lines.

A list of available colour maps for 3D plots, such as heatmaps, scatter and contour plots, can be found here: colour maps.

For a list of available scatter point styles, see here: scatter point styles.