Entering edit mode
7.3 years ago
LauferVA
4.1k
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