Hello Peng Yu, Sorry I misunderstood your question the first time. It is possible to do what you are asking. For your custom track, you will need to use BED format instead of bedGraph format. If you add the name field to your custom track data (column 3), that will push the score field to column 4. Then add "useScore=1" to your track definition line. Find the details here:
http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED http://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK Note that your score values will need to fall within the range of 0-1000. If you would like to display in a shade other than gray/black, set the color parameter like so: color=0,60,120 (shades of blue) color=100,50,0 (shades of brown) Here's an example you can try as a Custom Track: browser position chr19:59302001-59304701 browser hide all track name="Bed Format" description="Bed with shades of blue" visibility=dense windowingFunction=mean color=0,60,120 useScore=1 chr19 59302000 59302300 a 100 chr19 59302300 59302600 b 200 chr19 59302600 59302900 c 400 chr19 59302900 59303200 d 500 chr19 59303200 59303500 e 600 chr19 59303500 59303800 f 700 chr19 59303800 59304100 g 800 chr19 59304100 59304400 h 900 chr19 59304400 59304700 i 1000 I hope this information is helpful to you. Please don't hesitate to contact the mail list again if you require further assistance. Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu ----- Original Message ----- From: "Peng Yu" <[email protected]> To: "Ann Zweig" <[email protected]> Cc: [email protected] Sent: Tuesday, January 5, 2010 12:51:09 PM GMT -08:00 US/Canada Pacific Subject: Re: [Genome] How to show multiple tracks with the same color map (dense visibility)? I don't think I got my question answered. Please load the following data to the custom track, which choose 'dense' for both track "BedGraph Format" and "BedGraph Format1". The value ranges are different for these two tracks. But the gray scale ranges are the same for both tracks. What I am looking for is a consistent gray scale for both tracks (visibility=dense), i.e. for the same value, the gray scale in both tracks should be the same. I could do this by explicit specifying the color or gray scale in some format. But if there is a way to automatically do the value to color conversion by the genome browser, it will be more convenient to use. browser position chr19:59302001-59304701 browser hide all browser pack refGene encodeRegions browser dense altGraph # 300 base wide bar graph, autoScale is on by default == graphing # limits will dynamically change to always show full range of data # in viewing window, priority = 20 positions this as the second graph # Note, zero-relative, half-open coordinate system in use for bedGraph format track type=bedGraph name="BedGraph Format" description="BedGraph format" visibility=full color=200,100,0 altColor=0,100,200 windowingFunction=mean priority=20 chr19 59302000 59302300 -1.0 chr19 59302300 59302600 -0.75 chr19 59302600 59302900 -0.50 chr19 59302900 59303200 -0.25 chr19 59303200 59303500 0.0 chr19 59303500 59303800 0.25 chr19 59303800 59304100 0.50 chr19 59304100 59304400 0.75 chr19 59304400 59304700 1.00 track type=bedGraph name="BedGraph Format1" description="BedGraph format1" visibility=full color=200,100,0 altColor=0,100,200 windowingFunction=mean priority=20 chr19 59302000 59302300 0 chr19 59302300 59302600 0.25 chr19 59302600 59302900 0.50 chr19 59302900 59303200 0.75 chr19 59303200 59303500 1.0 chr19 59303500 59303800 1.25 chr19 59303800 59304100 1.50 chr19 59304100 59304400 1.75 chr19 59304400 59304700 2.00 On Tue, Dec 22, 2009 at 4:41 PM, Ann Zweig <[email protected]> wrote: > Hello Peng Yu, > > For some reason, your email got filtered out by our mail-list software. > > Yes, it is possible to do what you are asking: you can use the same > gray-scale for several tracks. And you can also use colors. For details on > the parameters needed, please see these two help documents: > > http://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK > http://genome.ucsc.edu/goldenPath/help/bedgraph.html > > To view an example of differently-colored positive and negative values, > load this Custom Track: > > browser position chr19:59302001-59304701 > browser hide all > browser pack refGene encodeRegions > browser full altGraph > # 300 base wide bar graph, autoScale is on by default == graphing > # limits will dynamically change to always show full range of data > # in viewing window, priority = 20 positions this as the second graph > # Note, zero-relative, half-open coordinate system in use for bedGraph > format > track type=bedGraph name="BedGraph Format" description="BedGraph format" > visibility=full color=200,100,0 altColor=0,100,200 windowingFunction=mean > priority=20 > chr19 59302000 59302300 -1.0 > chr19 59302300 59302600 -0.75 > chr19 59302600 59302900 -0.50 > chr19 59302900 59303200 -0.25 > chr19 59303200 59303500 0.0 > chr19 59303500 59303800 0.25 > chr19 59303800 59304100 0.50 > chr19 59304100 59304400 0.75 > chr19 59304400 59304700 1.00 > > > At this moment, the coloring for negative-valued bedGraphs is broken when > they are viewed with a "Windowing Function" set to "mean+whiskers". If you > specifically set the Windowing Function to mean, you will see the correct > coloring for both positive and negative values. > > This error has been fixed and will be patched into the website very early > next year. > > I hope this information is helpful to you. Please don't hesitate to > contact the mail list again if you require further assistance. > > > Regards, > > ---------- > Ann Zweig > UCSC Genome Bioinformatics Group > http://genome.ucsc.edu > > > > >> Subject: How to show multiple tracks with the same color map (dense >> visibility)? >> Sent By: "Peng Yu" <[email protected]> >> On: December 19, 2009 9:41 AM >> To: [email protected] >> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> >> I want to show multiple tracks (eg. the following one). The same gray >> scale represent different values in different tracks. Is there a way >> to use the same gray scale for the same value in different tracks? Is >> there a way to use different color rather than gray scale? >> >> >> >> browser position chr1:100-130 >> browser hide all >> browser pack refGene encodeRegions >> browser full altGraph >> track type=bedGraph name="name1" description="description1" >> visibility=dense >> chr1 101 102 1 >> chr1 111 112 2 >> chr1 121 122 3 >> track type=bedGraph name="name2" description="description2" >> visibility=dense >> chr1 101 102 -1 >> chr1 111 112 -2 >> chr1 121 122 -3 >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
