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
