Hi Torsten Many thanks for the feedback. These all look like excellent and useful ideas. We already have implemented a global min/max settings for the graphs. This is in the development version if you right click on the graph there is a 'Set Min/Max Values' option, you can get this from:
http://www.sanger.ac.uk/Software/Artemis/#development Also, in the latest version (v11) there is an option (when you read in the user plot file) to take the log of the values. Your other requests will certainly go on the to do list. Regards Tim On 5/14/09 4:55 AM, "Torsten Seemann" <torsten.seem...@infotech.monash.edu.au> wrote: > Tim et al, > > One of the hidden gems in Artemis is the ability to load "User plots". > We use this for all sorts of things, including viewing depth/coverage > of Illumina reads onto references, highlighting SNPs, and so on. They > are a rapid way to visualize new data sets related to the genome > sequence. > > I have three requests I hope you will consider: > > 1. Allow user plots to be specified on the command line, similar to > how features/entries can be added, but with another symbol (eg. @). > This would save plenty of fiddling with menus and file browsers. > > % art genome.gbk + features1.gff + features2.tab @ userplot1.txt @ > userplot2.txt ... > > > 2. Add logarithmic scaling or global clipping to the user plot options. > > Currently you can have "no scaling" or "dynamic scaling" (based on > current viewing window). I guess I would like the option of "global > scaling" (set a global min/max to clip to) or "logarithmic scaling" > (take log(1+x) for every value). This is because a single outlier > value/peak in the user plot data will swamp the detail in the rest of > the plot, and although dynamic scaling works around this, it is > confusing when you scroll through as the heights aren't graphically > comparable from window to window. > > > 3. Add features from DIPS in user plot > > Currently you can add features based on thresholded peak runs in a > user plot. Could you provide the same functionality for dips BELOW a > certain threshold? This could be used to mark low coverage zones in a > read-depth plot for example. Or perhaps this could be generalized to > any "band pass" filter with min and max thresholds. The peaks and dips > would be special case where min or max was -Inf or +Inf. > > > Thank you for reading my feedback, > > > --Torsten Seemann > --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash > University, AUSTRALIA > > _______________________________________________ > Artemis-users mailing list > Artemis-users@sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
