Question: 'ValueError: No usable data points to plot out of 0 probes, 0 segments, 0 variants' in Scatter Plot
0
gravatar for wei.wei
6 months ago by
wei.wei10
wei.wei10 wrote:

Hi,

I encountered this error while trying to do a scatter plot of a specified chromosome. Here's my command:

cnvkit.py scatter -s Sample1.cn{s,r} -c chr8

Here's the error I've gotten:

File "/Users/wwei/anaconda2/bin/cnvkit.py", line 13, in <module>
    args.func(args)
  File "/Users/wwei/anaconda2/lib/python2.7/site-packages/cnvlib/commands.py", line 914, in _cmd_scatter
    **scatter_opts)
  File "/Users/wwei/anaconda2/lib/python2.7/site-packages/cnvlib/scatter.py", line 49, in do_scatter
    y_min, y_max, title, segment_color)
  File "/Users/wwei/anaconda2/lib/python2.7/site-packages/cnvlib/scatter.py", line 237, in chromosome_scatter
    y_min=y_min, y_max=y_max, segment_color=segment_color)
  File "/Users/wwei/anaconda2/lib/python2.7/site-packages/cnvlib/scatter.py", line 381, in cnv_on_chromosome
    set_xlim_from(axis, probes, segments)
  File "/Users/wwei/anaconda2/lib/python2.7/site-packages/cnvlib/scatter.py", line 488, in set_xlim_from
    len(variants) if variants else 0))
ValueError: No usable data points to plot out of 0 probes, 0 segments, 0 variants

What are the probes, segments and variants referring to?

cnvkit • 219 views
ADD COMMENTlink modified 4 months ago by Biostar ♦♦ 20 • written 6 months ago by wei.wei10

Do you not have to run it like this:

cnvkit.py scatter Sample1.cnr -s Sample1.cns -c chr8 -o Sample1-scatter.pdf

Kevin

ADD REPLYlink modified 6 months ago • written 6 months ago by Kevin Blighe46k

I think both ways of writing mean the same thing? But both gave me the same error. lol

ADD REPLYlink written 6 months ago by wei.wei10

Okay, you may want to contact the developer of the program. Sometimes, he (the developer) is on Biostars, but not right now it seems.

ADD REPLYlink written 6 months ago by Kevin Blighe46k
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