Box I.10    Plotting with plot2_biogem_*.m scripts 

When you run one of the plot2_biogem_*.m plotting scripts, you will be asked a series of questions to set the variable to be displayed and various plotting parameters. Note that none of your answers should start or end with an under-score ('_'), and file-name extensions are not required. The sequence is as follows; 

The first line to appear is; 

> BioGeM plotting: hit ENTER to re-use previously set plotting variables 

as it says - if you have previously run a script, the values for each plotting parameter are saved, and if you don't want to change a value, just hit RETURN without entering anything. If there is no previous value and you try this, the script will be sure to let you know ... 

Next, you are asked for a 

> Time-slice identifier: 

which is simply the sub-string defining the date of the time-slice (e.g., 0100). 

The parameter to determine which variable you want to plot is now set (except in plot2_biogem_opsi.m); 

> Data identifier: 

to which you enter the sub-string corresponding to 'CATAGORY_TYPE' (see Box II.1). For example, for ocean temperature data, you would enter 'ocn_T'. 

The next question depends on which script you are using. For the k and i slice plotting scirpts, you are asked for the k and i slice 'value', respectively. For plot2_biogem_i_AVE.m you are asked for the 'Mask filename', whereas for plot2_biogem_k_INT.m and plot2_biogem_opsi.m you are not ask for anything. 

Now come a series of questions to scale the plot. First of all you are asked if you want to set a scaling factor or 'auto-scale' the plot. If you enter '0' for the scaling factor then the plot will be auto-scaled for you, with 10 contor intervals equally spaced between the minimum and maximum values that occur. This can be useful initially if you are unsure of the range of values of the data. Alternatively, to scale the data you enter a factor to multiply the data by; i.e., to get ocean tracer concentrations as mmol kg^-1 rather than mol kg^-1, you would enter '1000000' (or '1.0E6'). 

If you chose to scale the data (i.e., a non-zero value for the scaling factor), you then get asked three questions about the plotting range and number of contours (strictly - this is the number of color bands used in the color scale, with two extra added for >maximum and <minimum values). These are fairly self-evident; 

> Minimum contour value: 

> Maximum contour value: 

> Number of contours: 

The script will color-plot your data starting at the mimium value you specify up to the maximum value you specified, with a number of contour levels you have also supplied.