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
