Question: Locus Zoom issuing an error in valid.viewport()
0
gravatar for Vincent Laufer
3.3 years ago by
Vincent Laufer1.1k
United States
Vincent Laufer1.1k wrote:

I am attempting to run locuszoom, but it is drawing blank (all white) .pdf files.

Below I have reprinted the entire output for reference. Has anyone encountered an error with viewport before, or know why this would happen?

+---------------------------------------------+
| LocusZoom 1.3 (06/20/2014)                  |
| Plot regional association results           |
| from GWA scans or candidate gene studies    |
+---------------------------------------------+

Loading settings..
Options in effect are:

+------------+------------------------------------------------------------+
|   Option   |                           Value                            |
+------------+------------------------------------------------------------+
| epacts     | ICHIP_ZINB_SQRTDD_FOR_LZ_ZERO.txt                          |
| chr        | 2                                                          |
| start      | 204712807                                                  |
| end        | 204712807                                                  |
| build      | hg19                                                       |
| ld-measure | rsquare                                                    |
| pop        | AFR                                                        |
| source     | 1000G_March2012                                            |
| snpset     | Illu1M                                                     |
| gene-table | refFlat                                                    |
| cache      | ../ICHIP_ZINB_SQRTDD_FOR_LZ_ZERO.txt.2.204712807.204712807 |
+------------+------------------------------------------------------------+

Plotting parameters in effect are:

+-----------+------------+
|   Option  |   Value    |
+-----------+------------+
| markerCol | MarkerName |
| pvalCol   | P-value    |
+-----------+------------+

Using /home/tools/locuszoom/bin/locuszoom.R..
Beginning plotting sequence for: chr2_204712807-204712807
Extracting region of interest (chr2:204712807-204712807) from input file..
Attempting to find best SNP in region..
Found: chr2:204712807
Finding pairwise LD with reference SNP chr2:204712807..
Source: 1000G_March2012 | Population: AFR | Build: hg19
Using /share/apps/rc/software/PLINK/1.07-x86_64/plink to compute LD..
Warning: could not locate LD cache database, tried: ../ICHIP_ZINB_SQRTDD_FOR_LZ_ZERO.txt.2.204712807.204712807, creating new one..
Creating new LD cache branch for current LD source/population/build..
Grabbing annotations from SQLite database..
Creating plot..
Error in valid.viewport(x, y, width, height, just, gp, clip, xscale, yscale,  : 
  invalid 'xscale' in viewport
Calls: zplot -> dataViewport -> viewport -> valid.viewport
recover called non-interactively; frames dumped, use debugger() to view
[1] "Wed Dec 21 06:20:48 2016"
Deleting temporary files..
Time required: 0d:0h:3m:0s
locus zoom • 1.1k views
ADD COMMENTlink written 3.3 years ago by Vincent Laufer1.1k
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