# SIMPLOT: help and advice

Consult the reference manual for further details and worked examples.
W.G.Bardsley, University of Manchester, U.K.

Note: sv_simfit has a simplified version of this program with fewer options

- Run time options
- Plotting transformed data
- Miscellaneous plots
- Hardcopy and saving the plot settings for re-use
- Advice for first-time users

## SIMPLOT run-time options

On opening program SIMPLOT two options are available as follows.

First-time user

This opens SIMPLOT in VIEW/PLOT mode.

VIEW/PLOT mode allows you to choose a plot type whereupon you will be given the chance to plot a corresponding test file to see what the plot should look like, and also an opportunity to view the file format required to prepare your own data files for plots of this type.
Exit from this mode returns you to the main menu so you can choose another plot type to investigate.
However, for each plot type, you can choose to return to NORMAL mode and proceed with that plot type as an experienced user.

Experienced user

This opens SIMPLOT in NORMAL MODE.

Only select this option when you know which plot types you require and also understand how to select the appropriate test files using the [Demo] button on the FILE OPEN dialogue, or else you have prepared your own data files to input.
However, advanced users trying to display a plot type they are not familar with should choose to run in VIEW/PLOT mode as this can easily be switched off to return to NORMAL mode.

Summary

You can transfer data interactively from other Simfit programs, type in data directly from the keyboard, paste in data tables from the clipboard, or open data files, to create plots by editing the data, title, legends, line- and symbol-types, sizes, error bars, offsets, frames, marker text, keys, colours, arrows, etc. as required. First you read in all the data required for the overlays, and the program will make a default graph. The idea is then to change plotting parameters systematically, by editing/re-displaying, etc. until the graph is correct, before finally saving a graphics file, e.g. *.eps (for PostScript users), or *.png (for non-PostScript users), but *.emf, *.pcx, *.tif, *.jpg, *.pdf, or *.bmp files can also be created. Plot style details are stored in configuration files which can be edited interactively, but users can save their own configuration files to act as templates that can be used to over-ride the defaults.

## Plotting transformed data

You may wish to plot transformed data (e.g. Scatchard plots) but do not prepare the data as log(x),log(y) or 1/x,1/y, etc. Input original data as x, y coordinates, then pick the option to display in transformed axes, e.g. semilog, Hill plot, etc. which automatically re-scales your data and error bars. Once you have read in a set of files you can select which to display/edit/suppress, etc. at any stage.

Plots of y against x

You need files with x in column 1, and y in column 2, made using programs Makfil, Makmat or Makdat, or else saved from a spreadsheet program as ASCII coordinate plotting files. You can plot symbols only, lines joining up points, or else both lines and symbols at the same time. Practise with the test files simplot.tf1, simplot.tf2. and simplot.tf3.

Plots with error bars

If you read in a data file with all replicates, then you can use the [Data] option to generate error bars interactively. Otherwise, you input files with columns of x, lower-y-lim, mean-y, then upper-y-lim, which can be made by typing data directly into program Makmat. A better way is to read a Simfit master curve-fitting file (made by Makfil, with all x and y values, not means of replicates) into program Editfl then choose the option to rearrange into increasing order of x and create a file with means and selected error bars. The program will plot just upper/lower or both error bars but, to remove individual bars, set the corresponding con.lim. = mean. Practise with the test files errorbar.tf1 (which plots as standard error bars), and errorbar.tf2 (which plots as slanting, unsymmetrical, and multiple error bars).

Log-Odds plots from analysis of proportions

After calculating binomial probability parameter estimates p_hat = y/N and confidence limits using the analysis of proportions option with program SIMSTAT there is an option to plot the log odds, that is

         log_10[y/(N - y)] = log_10[p_hat/(1 - p_hat)

on the X-axis with the control variable x (usually group number, time or drug dose) on the Y-axis. If it wished to transfer these data to the advanced graphics options for editing it must be remembered that all such data must be transferred as separate data files for the original variables with Y coordinates for the y/(N - y) estimates and error bars but X coordinates for the control variable. So, in order to transform the data for editing in the advanced 2D editing interface the following steps must be taken.

1. Choose the reverse Y-semilog transform to replace the data supplied so that y values supplied are tranformed into log coordinates and plotted on the new X-axis while the x values supplied are plotted on the new Y-axis.
2. The X-legend must be renamed as log_10[y/(N - y)] or log_10(p/(1 - p)]
3. The Y-legend must be renamed as the control variable x
4. The data ranges and tic marks will have to be edited because the data ranges have altered
5. The plot title will have to be edited

Further editing and hardcopy saving can now be performed within the new reversed Y-semilog space.

## Miscellaneous plots

If you have just one vertical scale on the y-axis there is a wide variety of options for editing symbols, fonts, etc. Histograms, for example, can be plotted just like normal graphs, or as bar charts.

Double graphs (one x-scale, two y-scales)

This is a special graph type when you require two vertical y scales. For example, a left hand scale (Y-axis) for absorbance at 280nm from a chromatography column, and an extra y-scale (E-xtra) for enzyme activity eluted. To make this sort of graph, you must input two groups of data files, the first in the left hand units, and a second group requiring the right hand scale of units. Double graphs cannot have an information panel at the side, and they cannot be transformed interactively like standard graphs.

Cluster plots, Step graphs, Bar charts and Pie charts

For simple clusters/steps/bars, make files with required x,y values using Makfil, and select line/symbol types accordingly. For simple bar charts type in data or read in a matrix file. For simple pie charts type in data or read in a vector file. For advanced bar (or pie) charts, read in files formatted like barchart.tf1, or piechart.tf1, etc. Note that, after creating a bar (or pie) chart directly from a matrix file, it is transformed internally into a temporary advanced type of bar (or pie) chart file, which can be saved for re-use if required, using the [Data] option.

Exhaustive analysis of vectors and matrices

These options are very useful for exploring all the graph styles that can be created by Simfit from numerical tables. Exhaustive analysis of a vector is particularly useful for plotting piecharts or time series, while exhaustive analysis of a matrix is a very convenient technique for creating box and whisker plots or stacked bar charts.

3D-surfaces and 3D-bar charts for z = f(x,y)

You can make surface files for a mathematical model of the form z = f(x,y) using Makdat, or you can type in a n by m matrix of z values, or make files directly using Makmat. Practise with the test files surface.tf1, etc.

Parameteric and 3D-curves in space for x(t), y(t), z(t)

The procedure will be easily understood after using the test files called spiral.tf1, etc. 2D and 3D parametric curves can be also be plotted interactively if mathematical models of the form r = r(theta), x(t) with y(t), or x = x(t), y = y(t), z = z(t) can be defined for a 3D space curve.

## Hardcopy and saving the plot settings for re-use

Once you have selected line and symbol types, arrows, extra text, information panels keys, etc., you can write these to a configuration file for re-use. At any stage you can read in an existing configuration file to over-ride the current defaults. This rule does not apply to 3D-surfaces and curves in space. These options start with a set of defaults which let you see the plot if the files supplied are correctly formatted. From then on, any alterations you make will be remembered and used as defaults in configuration files for subsequent re-plotting.

Saving a metafile

After editing an advanced 2-dimensional plot you can save the result as a metafile.
These can be input back into SIMPLOT retrospectively to re-create the plot, which is a useful way to interrupt editing in order to return later and continue editing.

Data ranges and tick marks

The data supplied are used to determine initial estimates for appropriate x,y ranges and number of tick marks, that you can then adjust as required.

Moving graphical objects

To move objects such as extra text, arrows, information panels or bit-maps, etc., use the mouse to drag the arrow icon to the desired position and set up a current point, or hot spot, as indicated by the tip of the arrow icon. Then move the selected object to this current position.

PostScript hardcopy

The highest possible hardcopy quality is available for users who have PostScript facilities, as Simfit can drive PostScript printers directly or make encapsulated PostScript files (*.eps) that can be edited, or arranged into collages, using Editps. Users without PostScript printers can still benefit from Simfit PostScript features by using the ghostscript/gsview suite or the ghostscript dlls supplied with the SIMFIT package, which allows users to print PostScript files on non-PostScript printers.. With this software, improved graphics files can also be created in *.png, and *.pdf formats by transforming *.eps to *.pdf, etc.

Windows hardcopy

Simfit can drive printers directly, and there is a wide choice of formats for saving graphics files to include in documents. Enhanced metafiles (*.emf) can be used to save a graph as can bit map files (*.bmp) which are not recommended, as they are large and give poor resolution, but they can be easily used by painting programs or transformed into compressed formats (*.pcx, *.jpg, or *.tif).

The two best formats for Windows users are either portable network graphics (*.png) which are compressed bit-maps or scalable vector graphics (*.svg) which can be viewed at any magnification without loss of resolution, and both *.png and *.svg files are the standard format for internet use. The SIMFIT website has a gallery in standard *.png format and and a gallery in enlarged *.svg format along with examples of how *.svg files can be rescaled to change the aspect ratio without distorting fonts or plotting symbols.

## Advice for first-time users

From the advanced 2D graphics interface there is a [Help] button and pressing this gives a summary of all the methods available for editing SIMFIT graphs. The same information can also be accessed by using a right-mouse click within the plotting area of any SIMFIT graph. Also the reference manual and tutorials available in pdf format from the main SIMFIT menu provide more specialised information about graphics editing illustrated by many worked examples.

However, the best way to learn how to use this program is to run as an inexperieced user then read in the test files provided for the graph type of interest and experiment with the options available. For example:

- Choose a simple x,y graph then read in the library file called simplot.tfl (which uses simplot.tf1, .tf2, .tf3).
- Try transforming to double reciprocal, Scatchard, log y as a function of log x and so on.
- Experiment with changing the line and symbol types.
- Observe all the effects of horizontal, square, vertical formats, offsets, tick marks, frames and so on.
- See what happens when you request an information panel.
- Edit the title and introduce subscripts or superscripts, Greek, degrees centigrade, maths symbols, etc.
- Add some extra text and arrows to the plot.
- Save the current configuration to a configuration file.
- Exit then re-enter and read in the library file , then the configuration file to see how the previous settings are thereby restored.