Hi Jernej, As we discussed off-list, this problem appears to be corrected. Please let us know if you find any problems in the future, and thank you for your help.
-- Brooke Rhead UCSC Genome Bioinformatics Group On 09/05/09 03:06, Jernej Ule wrote: > Dear Brooke, > > Many thanks for this added functionality, it works great! Only one thing > - 'Always include zero' can only be used with one track at a time, > whereas I would often need to make figures that compare multiple tracks. > For now I will make the tracks individually and then copy them together > in Illustrator, but when you get a chance in the future, it will help to > be able to have multiple tracks with zero included > > Kind Regards, > Jernej > > > On Sep 5, 2009, at 1:38 AM, Brooke Rhead wrote: > >> Hello Jernej, >> >> We have added the functionality you requested to the wiggle track >> configure page, but it is only available on our test site at the >> moment. The test site is here: >> >> http://genome-test.cse.ucsc.edu >> >> On the wiggle track configuration page, look for a new "Always include >> zero: ON/OFF" line. Please let us know if you encounter any problems. >> >> Most likely, the new functionality will make it to our main site >> around September 21st. Be aware that there are a lot of experimental >> tracks that have not been through the QA process on the test site. >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> On 08/09/09 12:24, Jernej Ule wrote: >>> Thanks - in the meantime I'll artificially add data with y=0. Let me >>> know once this option is available. >>> Cheers, >>> Jernej >>> On Aug 7, 2009, at 11:37 PM, Brooke Rhead wrote: >>>> Hi Jernej, >>>> >>>> I see what you mean. You would like the y=0.0 line to be visible no >>>> matter what. This is an option that is not available currently. >>>> However, I have told our developers about it, and it is something >>>> that could possibly be implemented in the future. It will not >>>> likely happen anytime soon, though. >>>> >>>> Thanks for your clear explanation and suggestion. >>>> >>>> -- >>>> Brooke Rhead >>>> UCSC Genome Bioinformatics Group >>>> >>>> >>>> On 08/07/09 01:18, Jernej Ule wrote: >>>>> Dear Brooke >>>>> Many thanks for your advice. The example I explained was simplified >>>>> - your explanation now does solve it, however I have also a more >>>>> general problem. I want that the y axis always includes a 0, >>>>> regardless of data range, but at the same time, I want the >>>>> auto-scale to data view. I have both negative or positive data in >>>>> my Bedgraph, and depending on which genomic window one chooses, I >>>>> might have only negative or only positive values. I show an example >>>>> of negative values here: >>>>> ------------------------------------------------------------------------ >>>>> >>>>> I'd like the result to look more like this: >>>>> ------------------------------------------------------------------------ >>>>> >>>>> I was able to get this by adding a value 0 at position 6330. >>>>> I don't normally have 0 values in my data, so I'd prefer if there >>>>> was another way to get a 0 on the y axis. I tried setting the >>>>> following; >>>>> Draw y indicator lines: at y = 0.0: ON at y =0 >>>>> But it didn't make any difference, unless I had a 0 value in the >>>>> data, such as in the second case, where you now see a y line - >>>>> unfortunately, the y line at 0 doesn't show up in the first example >>>>> (even though the settings are the same!) >>>>> I'd appreciate your further advice. >>>>> Jernej >>>>> On Aug 6, 2009, at 8:56 PM, Brooke Rhead wrote: >>>>>> Hello Jernej, >>>>>> >>>>>> Thank you for searching the mailing list archives for an answer to >>>>>> your question. >>>>>> >>>>>> You can control the vertical viewing range on track controls page >>>>>> for your custom track. Click on either the blue track name, or on >>>>>> the thing blue/gray bar just to the left of your track in the >>>>>> Genome Browser image. You will be presented with several options >>>>>> for the display of your bedGraph track. Change the "Vertical >>>>>> viewing range" to min: 0 and max: 4, then set "Data view scaling" >>>>>> to "use vertical viewing range setting" (instead of "auto-scale >>>>>> data to view"). >>>>>> >>>>>> The items with a value of 1 should now take up one quarter of the >>>>>> vertical space in the track. >>>>>> >>>>>> -- >>>>>> Brooke Rhead >>>>>> UCSC Genome Bioinformatics Group >>>>>> >>>>>> >>>>>> On 08/06/09 04:16, Jernej Ule wrote: >>>>>>> Hi, >>>>>>> I still encounter the same problem as was described by a last >>>>>>> year's post: >>>>>>> https://lists.soe.ucsc.edu/pipermail/genome/2008-August/016943.html >>>>>>> It was supposed to be fixed, but is not. Or maybe my problem is >>>>>>> slightly different, so let me describe it. I have data ranging >>>>>>> from 1 to 4. The data with values of 1 do show up, but only as >>>>>>> very tiny dots. Instead I'd like the Y axis to start at 0, so >>>>>>> that the values with 1 reach up to one quarter of those with >>>>>>> values of 4. Can this be done? >>>>>>> Thanks, >>>>>>> Jernej >>>>>>> _______________________________________________ >>>>>>> Genome maillist - [email protected] >>>>>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
