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
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