It won't make any difference what type of wiggle format you choose. They all draw the same way.
You are going to have to provide me with a URL to your data file so I can see what it looks like. --Hiram ----- Original Message ----- From: "Lionel (Lee) Brooks 3rd" <[email protected]> To: "Hiram Clawson" <[email protected]> Cc: [email protected] Sent: Friday, April 1, 2011 11:16:42 AM Subject: Re: [Genome] bedgraph data will not display points Hi Hiram, >From http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format 1. Pseudo /line graphs/ can be drawn with the wiggle tracks by setting optional drawing parameters in the display of the track to draw /points/ instead of bars with smoothing on to smear the points together into a line. The pseudo line graph functionality is what I desire. Previously, it had been possible to do this with bedgraph format files. I don't know what "smearing" means. I'm just looking for a quick way to draw the moving average as I had been able to do before. As I mentioned below, my track line is: track type=bedGraph autoScale=on graphType=points windowingFunction=mean smoothingWindow=16 I suppose my solution is to modify my scripts to use the wiggle variable step format? thanks, -Lionel Hiram Clawson wrote: > Good Morning Lionel: > > The bedGraph drawing mechanism can construct bar graphs at your > specified intervals, or when you select graphType=points it will > draw only the top of the bar graph at your specified intervals. > There is no line drawing except by the trick of "smoothing" points > such that they appear to be in a line graph. This only works if > the data points are continuous when seen in the genome browser. > Smoothing will not smear points into areas where there is no > data value specified. > > The Genome Graphs function of the genome browser: > http://genome.ucsc.edu/cgi-bin/hgGenome > will only draw lines between your specified points. > > See also: > > http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format > > > --Hiram > > Lionel Brooks wrote: >> Hello all, >> >> I have a bedgraph file. In the past I have used to files to attain >> graphic output in the form of a smoothed line but I uploaded my most >> recent data set and now I cannot get a line graph. In fact, I'm not >> sure what I am looking at because the values that are displayed along >> the y-axis are not described with a label. >> Here is my track line: >> track type=bedGraph autoScale=on graphType=points >> windowingFunction=mean smoothingWindow=16 >> >> My data format is >> >> chr coordA coordB value >> >> Where approximate distribution of data values are : 5 <= value <= 500. >> Is it possible that your plotting function cannot compute this line >> because my coordinate intervals are too small? >> Another possibly relevant issue may be that the coordinate intervals >> are not fixed length. >> >> Any suggestions for course of action would be great. >> >> Sincerely, >> Lionel _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
