Hi
We are in the process of preparing a research article and have included an alternative Mapman representation of the carotenoid biosynthetic/catabolic pathway from grapevine (specifically for the newer Nimblegen grape arrays as well as the metabolites = carotenoids). We would like to make it available to the broader community and I need to know if this is possible, and if so, how do we go about it?
I have attached a png of the pathway representation.
Regards,
Philip

Dear Philip

thanks. So I reckon it is ok with you to make this publicly available immedeately.

Something else: Do you have this in a vectorized format: e.g. svg or Corel draw etc. As such a format would allow exporting the pathway in almost any resolution for journal figures.

Best Wishes,
Björn

Hi Bjorn

Thanks for the prompt reply. Yes we would like it available as soon as possible.

We have a pathway figure in png format, and an associated mapping file for the figure (in xls format with unique bin codes 99.1.4.01 through to 99.1.4.51). We would like to sort out some issues with the binning first (before making it available) and hope someone at Mapman could help...hopefully nothing major just a visualisation problem.

How would I get the figure in a vectorised format?

Regards,

Philip

Dear Philip

it is always best if it gets fully integrated, so let us know how we can help.

Regarding the vectorized format. This depends how you composed the image. If you made it in Powerpoint, Corel Draw etc. you could just send me the original file. If you composed it however in photoshop or somethign like this then there is nothing one can do.
(You can also find a short Faq what all this fuss about vectorized formats is about at http://mapman.mpimp-golm.mpg.de/pageman/help/help.html In brief if we never wanted to publish things in hardcopy journals it would probably not matter too much )

Cheers,
Björn

Hi Björn

Had a quick look and not too difficult for the svg conversion. I have it in Powerpoint so will send it on as such.

The problem is I can not get the heatmap representation if I have my experimental data in columns. Could only (counter-intuitively) get around it if we make a bin entry for each time-point...so if I have 3 time-points I have 3 bin entries per transcript and metabolite...3 identical bin codes with 3 different "identifiers" per transcript/metabolite.This makes it less useful since the bin has to change for each different experiment. It works if I want a line graph; just not a heatmap. Will appreciate any help/advice.

Regards,

Philip

Dear Philip

excellent.
If you want to get a heatmap of individual bins you can use the PageMan module. Right click on the experiment set and then choose show in PageMan. In the stats section choose the average module so it averages per bin.

If you use the old stand-alone PageMan version you can also directly fake heatmap by preparing a file likes this:

"Just put some random identifier code in column 1 and always finish with a column containing 1 and one containing 0. As of PageMan version 0.12 PageMan autodetects experiment files to be represented as heatmaps and adds the additional data." Then load the data in PageMan.
This is probably something to add as a core moduule to MapMAn to make it a bit more user friendly.

Best wishes,
Björn

Hi Björn

I tried what you suggested. With Pageman I get the heatmap representation, but lose the pathway visualisation.

Regards,

Philip