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? 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. 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. 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 ) 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. 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. '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. Source.


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Last Modified: April 23, 2016 @ 5:03 pm