Enlarging the graphical output of ensemble NMA calculations

[Former user]

I performed an ensemble NMA and wanted to include the results in my paper. The graphical output that is being produced is extremely small...especially I would like to make the lines in the graph thicker for publication purposes. please help me with the arguments. I searched the index but could not get hold of any that can manipulate the line width of the graph.

command plot(modes,pdbs=pdbs,col=col,spread=TRUE,offset=1,polygon=FALSE,label=c('M.tb','','S.la','','E.co','','S.pn','','C.su','A.ba','P.ae','P.fl'))

Any other arguments which can specify the magnification of the lines in the fluctuation plot will be helpful.

I have attached the graphical output for your reference.

Thank you.

[Barry Grant]

Try adding the lwd=3 paramater adjusting the number to your needs.

Note that this is a standard base graphics paramater that you can find documented in plot.default() and elsewhere

[jay]

This is the graphical output.

[jay]

Dear Sir,

As you can see (the attached PDF format of the graph), the graph is actually a spread one having 8 individual graphs.

Increasing the lwd to 3 increases only the first graph's bar width (the shaded area inside the first graph) and not the line width of the line graph.

Please help me as this graph is a vital part in my paper.

Thank you.

[Xinqiu Yao]

Hi,

The lwd is not passed to the lines. You could change line widths by modifying the source code in plot.fluct.R, the line containing lines(yvals[grp.inds[j] ..., adding lwd=2 (or whatever value you want). Then source the file by source('plot.fluct.R'), and try it again.

You could also try generating a smaller PDF to have thicker lines, e.g. pdf(file='XXX', width=3, height=3).

Or, you could modify lines directly with graphic software such as Illustrator.

Hope it helps...