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Author SHA1 Message Date
depristo b57a0a0310 improvements to the report code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4280 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 00:45:13 +00:00
kiran dfdd0b69a9 Removed unused dependency (it was causing a problem by looking for an X11 connection that didn't necessarily exist). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4244 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 19:56:00 +00:00
depristo 594fb4a547 More plots in report 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4225 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 02:56:51 +00:00
kiran 19e22cfa87 Fixed a bug where the script looked for the wrong column name. Also, all results are now returned in a single plot. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4216 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-06 14:19:57 +00:00
depristo 0c54bf4195 Better reporting and now with a special mode for listing exceptions 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4183 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-01 16:19:51 +00:00
corin cdad243645 updated version of the DPR. Now produces part of the tearsheet as well as good depth of coverage figures 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4182 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-01 15:38:58 +00:00
depristo fc5caa98a5 Improved reporting now with metrics by day/week/etc. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4180 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-01 02:43:13 +00:00
depristo 8683087756 Suppl. tools for working with and displaying GATK run reports 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4176 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-31 20:32:22 +00:00
kiran e14a347e2e Now prints cluster report to a single PDF, rather than a dozen different PDFs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4164 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-29 18:58:39 +00:00
kiran fd19c63aaf A data structure that allows data to be collected over the course of a walker's computation, then have that data written to a PrintStream such that it's human-readable, AWK-able, and R-friendly (given that you load it using the GATKReport loader module). 
This object designed to be both the structure that holds data during the execution of the walker, as well as the object that properly formats and emits the data so that it can be easily loaded into R.  In the end, you get a table that looks like this:

##:GATKReport.v0.1 ErrorRatePerCycle : The error rate per sequenced position in the reads
cycle  errorrate.61PA8.7         qualavg.61PA8.7
0      0.007451835696110506      25.474613284804366
1      0.002362777171937477      29.844949954504095
2      9.087604507451836E-4      32.87590975254731
3      5.452562704471102E-4      34.498999090081895
4      9.087604507451836E-4      35.14831665150137
5      5.452562704471102E-4      36.07223435225619
6      5.452562704471102E-4      36.1217248908297
7      5.452562704471102E-4      36.1910480349345
8      5.452562704471102E-4      36.00345705967977
...

A GATKReport object can hold multiple tables, and the write() method will emit all tables in succession.  Each table starts with its own ##:GATKReport.v0.1 table header, so each table can stand alone.  This allows for tables to be mixed and matched in a single file, or for the output from different walkers to be combined into a single file with no ill effect.

The display property of individual columns can be turned off.  This is useful when a column is used to store intermediate results, necesary for the computation of some later value, but the contents of the intermediate column itself are not required in the final output file.

Finally, the GATKReportTable allows for some simple, mathematical, element-wise and column-wise operations.  For instance, two whole columns can be divided, the results of the operation being stored in a third column.  This mimics the most basic of R operations, where whole vectors can be added, subtracted, multiplied or divided without requiring the developer to explicitly write a loop.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4159 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-29 05:39:24 +00:00
corin 8931a63588 updated a whole bunch of column names to work like i want them to and added more informative figures for DOC 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4131 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-26 18:19:09 +00:00
kiran fba71e3c15 Placeholder commit. Implements a loader for a new multi-part GATK reporting format. See what it looks like at /home/radon01/kiran/scr1/projects/NewVariantEvalOutput/results/v1/tableexample.txt . Still need to address the issue where numeric columns are being interpreted as a vector of strings, not numbers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4115 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-25 18:48:44 +00:00
corin 8054b6b295 Changing a name of a column for variantevals output for easier reading by R--let me know if this needs to be updated elsewhere; it's just a space to an underscore. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4062 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-19 19:18:16 +00:00
depristo ede87a03c2 Nicer plotting routine for tranches. Add a third arg to suppress the legend. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4049 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-17 19:20:58 +00:00
depristo e0abb73fd7 plot now assumes 1 / 1000 is the min error rate, not 1/100 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4010 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-11 14:48:22 +00:00
kiran 6037443e55 Handle interactive and non-interactive modes more elegantly. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4009 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-11 02:38:53 +00:00
kiran a7409df1a6 Be more robust to missing or empty files in VariantEval output. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4008 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-11 02:22:50 +00:00
depristo 67063deb16 Removed coloring by mixture weight. Each cluster gets a distinct color, and the legend indicates which cluster has which id and its weight 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4001 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-10 14:28:24 +00:00
depristo 672bee295c now plots tranches separately from optimizer 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4000 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-10 12:02:52 +00:00
depristo 41fee2d75e Publication tranches report is now the default output 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3967 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-07 13:58:59 +00:00
depristo f4ffef4479 Default max variants is now 5000 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3966 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-07 13:58:32 +00:00
depristo b63d64bbbc Beautiful labels, better choice of dimension ranges. Supports fast loading of just first N records for testing. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3964 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-06 23:17:32 +00:00
depristo d3bebe0f2c Reasonable comment 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3963 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-06 22:03:55 +00:00
depristo bb5dfd7e5e Slightly nicer plotting; not yet complete 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3961 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-06 20:01:31 +00:00
depristo 70f492a6e8 Prints out trivial debugging info 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3957 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-06 13:24:21 +00:00
kiran 1a36cb9296 Can now set the maximum number of variants to see in a cluster plot (useful when you don't need to see a billion points to get an idea of what's going on. Limit applies to known and novel variants separately. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3937 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-04 18:45:24 +00:00
kiran bd27287fe7 An R module that takes in a Variant Recalibration cluster file (file with '@!CLUSTER' lines in it), a tabularized VCF, and optionally a set of loci that should be examined more carefully, and emits a tremendous number of plots. For every annotation used in clustering, the distributions and pair-wise comparison (with ellipses denoting the 2-sigma cluster boundaries) are shown. Each cluster is shaded with a color proportional to its mixture coefficient. 
To use this module, you'll first have to take your VCF and create an R-readable table out of it with the following command:

python /path/to/Sting/trunk/python/vcf2table.py -f CHROM,POS,ID,AC,AF,AN,DB,DP,HRun,MQ,MQ0,MyHaplotypeScore,QD,SB my.vcf > my.vcf.table

Then, simply invoke this module with the command:

Rscript /path/to/Sting/trunk/R/VariantRecalibratorReport/VariantRecalibratorReport.R /path/to/output/prefix /path/to/my/my.clusters /path/to/my.vcf.table [/path/to/my.suspicious.loci]

This will create a number of plots all with the prefix "/path/to/output/prefix".  For instance, if you used QD, SB, HRun, and MyHaplotypeScore annotations during clustering, you should see output like this:

    /path/to/output/prefix.anndist.HRun.pdf
    /path/to/output/prefix.anndist.MyHaplotypeScore.pdf
    /path/to/output/prefix.anndist.QD.pdf
    /path/to/output/prefix.anndist.SB.pdf
    /path/to/output/prefix.cluster.HRun_vs_MyHaplotypeScore.pdf
    /path/to/output/prefix.cluster.HRun_vs_QD.pdf
    /path/to/output/prefix.cluster.HRun_vs_SB.pdf
    /path/to/output/prefix.cluster.MyHaplotypeScore_vs_HRun.pdf
    /path/to/output/prefix.cluster.MyHaplotypeScore_vs_QD.pdf
    /path/to/output/prefix.cluster.MyHaplotypeScore_vs_SB.pdf
    /path/to/output/prefix.cluster.QD_vs_HRun.pdf
    /path/to/output/prefix.cluster.QD_vs_MyHaplotypeScore.pdf
    /path/to/output/prefix.cluster.QD_vs_SB.pdf
    /path/to/output/prefix.cluster.SB_vs_HRun.pdf
    /path/to/output/prefix.cluster.SB_vs_MyHaplotypeScore.pdf
    /path/to/output/prefix.cluster.SB_vs_QD.pdf



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3936 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-04 18:35:14 +00:00
kiran b990a22bac A very nice way of automatically plotting the results of a VariantEval run. All of the hard work is actually in the common R repository, gsacommons.R, including methods for creating a Venn diagram. It also provides a mechanism for the output of a VariantEval run to be loaded into a single list object. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3828 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-19 12:38:26 +00:00
depristo 6ffcaa0afe Can run R scripts on the command line 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3750 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-09 00:13:18 +00:00
depristo 66931d433c useful routines for R 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3685 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 16:38:49 +00:00
corin bcab0eba01 This replaces tearsheet.r, neatens up graphics, and allows the script to be used in R's interactive environment 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3625 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-24 01:02:58 +00:00
corin ae88630d52 This script produces tearsheet and data processing report figures and tables when given Squid and Firehose produced data 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3594 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-18 21:36:29 +00:00
corin a2c266bda3 This script accpets file paths to analysis metrics tables and produces tearsheet data and data processing report graphs 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3585 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-18 13:02:25 +00:00
corin 266a47d83d This file automaticially generates data and graphics for tearsheets and data processing reports 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3551 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-14 18:39:23 +00:00
rpoplin 290771a8c2 Automatic cutting of recalibrated variant calls using ApplyVariantCuts. VariantRecalibrator produces the tranches plot alongside the optimization curve. Specify the levels using -tranche 1.0 -tranche 5.0 etc 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3472 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 15:03:00 +00:00
rpoplin 33a9549896 Variant Optimizer accepts a dbSNP rod arugment to use in determining known/novel status as opposed to using the rsID in the vcf record. VO generates plots of annotation values used in clustering broken out by knowns and novels. Useful for showing which annotations are approximately Gaussian. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3332 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-09 16:48:07 +00:00
chartl dc802aa26f Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3090 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-29 13:32:00 +00:00
rpoplin 06a212e612 Adding VariantConcordanceROCCurveWalker to create ROC curves comparing concordance between optimized call sets and validation truth sets in VCF format in order to evaluate performance of variant optimizer independently of achieving a particular novel ti/tv ratio. Added option to ignore only the specified filters in the input call sets via --ignore_filter <String>. Added option to provide a prior estimate of error for known snps via --known_prior <qual>. The het and hom calls are clustered independently. Infrastructure in place to use titv of known snps to inform p(true) of novel snps. Tweaked protection against overfitting based on suggestions from several people. Minor edits to AnalyzeAnnotations. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3071 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-24 19:43:10 +00:00
rpoplin c78fc23ec5 Minor updates to output of variant optimizer. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3031 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 12:46:47 +00:00
rpoplin 58a31bab6a Variant optimizer now outputs VCF files via ApplyVariantClustersWalker. Documentation to be added to the wiki. It is ready to be used by other people but only with great caution. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3028 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 20:41:42 +00:00
rpoplin 933823c8bc Removed the StingException when mkdir fails for Sendu in AnalyzeCovariates. Incremental updates to VariantOptimizer. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3013 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 19:45:02 +00:00
chartl ee68e38e02 Eliminate the shell items, as FH will be calling this with /broad/tools/apps/R-2.72/bin/Rscript 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2968 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 20:15:21 +00:00
chartl aa7191353a PlotDepthOfCoverage now produces a set of useful QC plots. Currently a first-draft, and it is unclear how the visualization will scale with increasing sample size and/or depth. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2962 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 16:42:35 +00:00
chartl 81ffb8243d Waypoint commit of plotting R script for Depth Of Coverage/Coverage Statistics 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2958 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 21:42:51 +00:00
kshakir 36129e01e4 Using bitmap() instead of png() since the former doesn't rely on X11. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2873 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-23 05:31:51 +00:00
kshakir 3738b76320 Added a playground concordance analyzer for summarizing VariantEval across a group. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2867 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-22 20:28:52 +00:00
chartl f02e94ab6f Eliminate the rescale factor -- heatmap automatically normalizes the data 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2845 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-16 16:34:33 +00:00
chartl 37fa1bf0cc Added heatmap function 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2843 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-16 15:12:54 +00:00
chartl 951b7a2433 First of what will be an increasingly useful set of tools, compiled into one command-line runnable library -- the goal is to have one plotting library that's callable because of limitations on the number of files you can package with a GenePattern module. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2841 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-15 16:51:47 +00:00
rpoplin 233a652161 Making the dotted quartile lines more clear. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2772 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-03 22:23:09 +00:00