[Patchwork-commits] r129 - pkg/patchwork/R www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Apr 27 15:49:04 CEST 2012
Author: sebastian_d
Date: 2012-04-27 15:49:04 +0200 (Fri, 27 Apr 2012)
New Revision: 129
Modified:
pkg/patchwork/R/patchwork.plot.r
www/AI_Cov.php
www/cg_exec.php
www/cg_resu.php
www/index.php
www/intro.php
www/pw_exec.php
www/pw_requ.php
www/pw_resu.php
Log:
Small updates to homepage text content
Modified: pkg/patchwork/R/patchwork.plot.r
===================================================================
--- pkg/patchwork/R/patchwork.plot.r 2012-04-23 08:46:31 UTC (rev 128)
+++ pkg/patchwork/R/patchwork.plot.r 2012-04-27 13:49:04 UTC (rev 129)
@@ -117,7 +117,8 @@
xlim=c(0,2.4),
ylim=c(0.1,1))
cat("Plotting Complete \n")
- cat("Shutting down..... \n")
+ cat("patchwork.plot Complete.\n")
+ cat("Below you may see some warning messages, you can read about these on our homepage. They are nothing to be worried about. \n")
}
\ No newline at end of file
Modified: www/AI_Cov.php
===================================================================
--- www/AI_Cov.php 2012-04-23 08:46:31 UTC (rev 128)
+++ www/AI_Cov.php 2012-04-27 13:49:04 UTC (rev 129)
@@ -182,7 +182,7 @@
Coverage is measured as total DNA content and normalized around 1. You will get a
clearer picture at higher coverage data, 120x etc, however patchworkCG has high quality results
- with low coverage also.
+ with low coverage aswell.
</div>
<div class="clear"></div>
Modified: www/cg_exec.php
===================================================================
--- www/cg_exec.php 2012-04-23 08:46:31 UTC (rev 128)
+++ www/cg_exec.php 2012-04-27 13:49:04 UTC (rev 129)
@@ -9,7 +9,7 @@
patchwork.CG.plot() is a function that visualizes allele-specific copy numbers from the
whole-genome sequenced data of tumors. <br /><br />
It is recommended that you run patchworkCG from a "clean" working directory.
-In this way you do not run the risk of having files write over eachother when
+This prevents the risk of having files write over eachother when
you run multiple different samples.<br /><br />
In the R environment load the patchworkCG library: <br />
@@ -105,28 +105,28 @@
patchwork.CG.copynumbers(cn2,delta,het,hom,maxCn=8,ceiling=1,name="copynumbers_",
CGfile=NULL,forcedelta=F)
-Arguments:
+ Arguments:
- cn2: The approximate position of copy number 2, diploid, on total
- intensity axis.
- delta: The difference in total intensity between consecutive copy
- numbers. For example 1 and 2 or 2 and 3. If copy number 2
- has total intensity ~0.6 and copy number 3 har total
- intensity ~0.8 then delta would be 0.2.
- het: Allelic imbalance ratio of heterozygous copy number 2.
- hom: Allelic imbalance ratio of Loss-of-Heterozygosity copy number
- 2.
- maxCn: Highest copy number to calculate for. Default is 8.
- ceiling: Default is 1.
- name: Default is "copynumbers_". The name you want attached to generated
- plots.
- CGfile: Default is NULL. If your CG.Rdata file is not in your working
- directory, and you dont wish to move it to your working
- directory, you can simply input the path here as CGfile =
- "path/to/file/CG.Rdata" so patchwork.CG.copynumbers() can find its
- data.
-forcedelta: Default is FALSE. If TRUE the delta value will be absolute
- and not subject to adjustments.
+ cn2: The approximate position of copy number 2, diploid, on total
+ intensity axis.
+ delta: The difference in total intensity between consecutive copy
+ numbers. For example 1 and 2 or 2 and 3. If copy number 2
+ has total intensity ~0.6 and copy number 3 har total
+ intensity ~0.8 then delta would be 0.2.
+ het: Allelic imbalance ratio of heterozygous copy number 2.
+ hom: Allelic imbalance ratio of Loss-of-Heterozygosity copy number
+ 2.
+ maxCn: Highest copy number to calculate for. Default is 8.
+ ceiling: Default is 1.
+ name: Default is "copynumbers_". The name you want attached to generated
+ plots.
+ CGfile: Default is NULL. If your CG.Rdata file is not in your working
+ directory, and you dont wish to move it to your working
+ directory, you can simply input the path here as CGfile =
+ "path/to/file/CG.Rdata" so patchwork.CG.copynumbers() can find its
+ data.
+ forcedelta: Default is FALSE. If TRUE the delta value will be absolute
+ and not subject to adjustments.
</pre>
To infer the arguments for patchwork.CG.copynumbers() you will need to look at one of the chromosomal
@@ -143,7 +143,7 @@
The <b>delta</b> argument is the difference between two copynumbers on the coverage axis. In this example we
used copy number 2 and copy number 3, but we could as well have used copy number 2 and the unmarked copy number
1 to the left of copy number 2. Delta does not take negative argument input. In this example delta is ~0.28.<br />
-The <b>het</b> argument is the position of heterzygous copy number 2 on the allelic imbalance axis. In this example
+The <b>het</b> argument is the position of heterozygous copy number 2 on the allelic imbalance axis. In this example
het is ~0.21.<br />
The <b>hom</b> argument is the position of homozygous, loss-of-heterozygosity, copy number 2 on the allelic imbalance
axis. In this example hom is ~0.79. <br /><br />
Modified: www/cg_resu.php
===================================================================
--- www/cg_resu.php 2012-04-23 08:46:31 UTC (rev 128)
+++ www/cg_resu.php 2012-04-27 13:49:04 UTC (rev 129)
@@ -81,7 +81,8 @@
Another example; if a segments total copy number is 3 and minor copy number is 0 then
that segment of the chromosome has 3 paternal OR 3 maternal copies.
-<br /><br />For more background information please read our submitted article!
+<!-- Uncomment when article is out.
+<br /><br />For more background information please read our submitted article! -->
<br /><br /><div style="text-align:center;"><a href="#top" style="text-decoration:none;">Top</a></div>
Modified: www/index.php
===================================================================
--- www/index.php 2012-04-23 08:46:31 UTC (rev 128)
+++ www/index.php 2012-04-27 13:49:04 UTC (rev 129)
@@ -10,7 +10,7 @@
<meta name="description" content="Tutorial and information regarding Patchwork and PatchworkCG, an allele-specific visualization tool developed for cancer genomes." />
<meta name="author" content="Sebastian DiLorenzo" />
-<meta name="keywords" content="Cancer,patchwork,patchworkCG,CompleteGenomics,R,visualization,Sequencing" />
+<meta name="keywords" content="Cancer,patchwork,patchworkCG,CompleteGenomics,R,visualization,Sequencing,Rforge,NGS,WGS,Allelic,Imbalance,Coverage,Allele-specific,Copy number" />
<script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jquery/1.6.4/jquery.min.js"></script>
<noscript>
Modified: www/intro.php
===================================================================
--- www/intro.php 2012-04-23 08:46:31 UTC (rev 128)
+++ www/intro.php 2012-04-27 13:49:04 UTC (rev 129)
@@ -12,7 +12,7 @@
Patchwork is available in two formats. The first, named simply patchwork,
-takes BAM files as its input whereas patchworkCG takes input from CompleteGenomics files. Detailed guides and information regarding these can be
+takes BAM files as input whereas patchworkCG takes input from CompleteGenomics files. Detailed guides and information regarding these can be
found in their respective tabs.
<br /><br />
Modified: www/pw_exec.php
===================================================================
--- www/pw_exec.php 2012-04-23 08:46:31 UTC (rev 128)
+++ www/pw_exec.php 2012-04-27 13:49:04 UTC (rev 129)
@@ -10,7 +10,7 @@
whole-genome sequenced data of tumors.<br /><br />
It is recommended that you run patchwork from a "clean" working directory to avoid the risk
- of having files write over eachother when you run multiple different samples.<br /><br />
+ of having files write over eachother if you run multiple different samples.<br /><br />
Execution may take quite a while depending on the size of your sample!
So if possible run it on a dedicated computer.<br /><br />
@@ -31,29 +31,29 @@
Excerpt from ?patchwork.plot regarding usage and arguments: <br />
<pre>
-Usage:
+ Usage:
- patchwork.plot(BamFile,Pileup,reference=NULL,normal.bam=NULL,normal.pileup=NULLAlpha=0.0001,SD=1)
-
-Arguments:
+ patchwork.plot(BamFile,Pileup,reference=NULL,normal.bam=NULL,normal.pileup=NULLAlpha=0.0001,SD=1)
+
+ Arguments:
- BamFile: Aligned, Sorted Bam-file.
- Pileup: Pileup file generated through samtools -vcf reference.fasta
- bamfile > outfile.
-reference: Default is NULL. Path to a reference file that can be
- created using patchwork.createreference() or downloaded from
- patchworks homepage.
-normal.bam: Default is NULL. The matched normal sample of the your
- BamFile.
-normal.pileup: Default is NULL. The pileup of your normal sample.
- Alpha: Default 0.0001, change if you want to try to get a better
- segmentation from patchwork.segment(). From DNAcopy
- (?segment): alpha: significance levels for the test to accept
- change-points.
- SD: Default 1, change if you want to try to get a better
- segmentation from patchwork.segment(). From DNAcopy
- (?segment): undo.SD: the number of SDs between means to keep
- a split if undo.splits="sdundo".
+ BamFile: Aligned, Sorted Bam-file.
+ Pileup: Pileup file generated through samtools -vcf reference.fasta
+ bamfile > outfile.
+ reference: Default is NULL. Path to a reference file that can be
+ created using patchwork.createreference() or downloaded from
+ patchworks homepage.
+ normal.bam: Default is NULL. The matched normal sample of the your
+ BamFile.
+ normal.pileup: Default is NULL. The pileup of your normal sample.
+ Alpha: Default 0.0001, change if you want to try to get a better
+ segmentation from patchwork.segment(). From DNAcopy
+ (?segment): alpha: significance levels for the test to accept
+ change-points.
+ SD: Default 1, change if you want to try to get a better
+ segmentation from patchwork.segment(). From DNAcopy
+ (?segment): undo.SD: the number of SDs between means to keep
+ a split if undo.splits="sdundo".
</pre>
@@ -174,6 +174,7 @@
Plotting Complete
Shutting down.....
Warning messages:
+ (Some warning messages about trying to load the files in the checklist below is not uncommon)
</pre>
If you did it correctly it should have generated similar output as can be seen above.
@@ -205,7 +206,7 @@
patchwork.copynumbers() is a function that determines which relationship between coverage
- and allelic imbalance signifies which copy number and allele ratio for each segment. <br /><br />
+ and allelic imbalance signifies what copy number and allele ratio for each segment. <br /><br />
The only file you absolutely must have in your working for the next part of execution is copynumbers.Rdata. <br /><br />
@@ -218,27 +219,27 @@
Excerpt from ?patchwork.copynumbers regarding usage and arguments: <br />
<pre>
-Usage:
+ Usage:
- patchwork.copynumbers(cn2,delta,het,hom,maxCn=8,ceiling=1,forcedelta=F)
-
-Arguments:
+ patchwork.copynumbers(cn2,delta,het,hom,maxCn=8,ceiling=1,forcedelta=F)
+
+ Arguments:
- name: Default is "copynumbers_". First part of output name for plots
- generated from patchwork.copynumbers().
- cn2: The approximate position of copy number 2,diploid, on total
- intensity axis.
- delta: The difference in total intensity between consecutive copy
- numbers. For example 1 and 2 or 2 and 3. If copy number 2
- has total intensity ~0.6 and copy number 3 har total
- intensity ~0.8 then delta would be 0.2.
- het: Allelic imbalance ratio of heterozygous copy number 2.
- hom: Allelic imbalance ratio of Loss-of-heterozygosity copy number
- 2.
- maxCn: Highest copy number to calculate for. Default is 8.
- ceiling: Default is 1.
- forcedelta: Default is FALSE. If TRUE the delta value will not be
- subject to small adjustment changes.
+ name: Default is "copynumbers_". First part of output name for plots
+ generated from patchwork.copynumbers().
+ cn2: The approximate position of copy number 2,diploid, on total
+ intensity axis.
+ delta: The difference in total intensity between consecutive copy
+ numbers. For example 1 and 2 or 2 and 3. If copy number 2
+ has total intensity ~0.6 and copy number 3 har total
+ intensity ~0.8 then delta would be 0.2.
+ het: Allelic imbalance ratio of heterozygous copy number 2.
+ hom: Allelic imbalance ratio of Loss-of-heterozygosity copy number
+ 2.
+ maxCn: Highest copy number to calculate for. Default is 8.
+ ceiling: Default is 1.
+ forcedelta: Default is FALSE. If TRUE the delta value will not be
+ subject to small adjustment changes.
</pre>
@@ -257,7 +258,7 @@
The <b>delta</b> argument is the difference between two copynumbers on the coverage axis. In this example we
used copy number 2 and copy number 3, but we could as well have used copy number 2 and the unmarked copy number
1 to the left of copy number 2. Delta does not take negative argument input. In this example delta is ~0.28.<br />
-The <b>het</b> argument is the position of heterzygous copy number 2 on the allelic imbalance axis. In this example
+The <b>het</b> argument is the position of heterozygous copy number 2 on the allelic imbalance axis. In this example
het is ~0.21.<br />
The <b>hom</b> argument is the position of homozygous, loss-of-heterozygosity, copy number 2 on the allelic imbalance
axis. In this example hom is ~0.79. <br /><br />
Modified: www/pw_requ.php
===================================================================
--- www/pw_requ.php 2012-04-23 08:46:31 UTC (rev 128)
+++ www/pw_requ.php 2012-04-27 13:49:04 UTC (rev 129)
@@ -17,7 +17,7 @@
</ul>
The Human Genome fasta files can be found in many places. Here is a link for 1000genomes hosted
-HG19 <a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gzv"
+HG19 <a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/"
target="_blank" style="text-decoration:none;">(human_g1k_v37)</a>. <br />
You probably also used such a file when aligning your tumor sequence.<br /><br />
@@ -45,7 +45,7 @@
<h4>patchwork.createreference()</h4> <br />
-This function creates a reference for you using a pool of samples of your selection.
+This function creates a reference using a pool of samples of your selection.
Choosing the samples to use for reference creation you should consider these factors:
<ul>
@@ -54,7 +54,7 @@
<li>They should be non-tumerous</li>
</ul>
-It is recommended that you use atleast 3 BAM files to create your own reference.
+It is recommended that you use atleast 3 BAM files to create your reference.
<br /><br />
Initiate R and load the patchwork and patchworkData libraries: <br />
@@ -113,7 +113,7 @@
error</a> is displayed.<br /><br />
-To Pileup either your normal sample or tumor sample BAM files: <br />
+To pileup either your normal sample or tumor sample BAM files: <br />
<pre>
samtools pileup -vcf <humangenome>.fasta <tumor/normalfile>.bam > pileup
Modified: www/pw_resu.php
===================================================================
--- www/pw_resu.php 2012-04-23 08:46:31 UTC (rev 128)
+++ www/pw_resu.php 2012-04-27 13:49:04 UTC (rev 129)
@@ -23,7 +23,7 @@
We can use this information to determine the clusters probable copy number
and allele content.<br /><br />
-The far left tiny cluster, on Total intensity axis, is the deletions, copy number 1.
+The far left tiny cluster, on Coverage axis, is the deletions, copy number 1.
Moving to the right the next two clusters, lower cluster is quite small,
are the allelic states of copy number 2. Following this reasoning the next set of clusters
must be copy number 3, then 4 etc. The average copy number for the sample is just above 3.
@@ -31,7 +31,7 @@
This arrangement of the genome is easier to see from one of the plots generated by
patchwork.copynumbers() or in our section above on allelic imbalance, however before using
that function you will need to be able to determine the constitution of the tumor
- genome as it is used as input arguments patchwork.copynumbers!
+ genome as it is used as input arguments for patchwork.copynumbers()!
<img id="fig2pw" src="css/img/tumor.bam_karyotype.chr18.png" alt="Results example patchwork.plot"
title="Figure 2 patchwork"
@@ -40,12 +40,12 @@
<h5>Middle part of the plot</h5>
-The chromosome in questions coverage plotted against the position on the chromosome.
+The chromosome in questions coverage plotted against the chromosomes coordinates.
<h5>Bottom part of the plot</h5>
The chromosome in questions allelic imbalance plotted against the
-position on the chromosome.
+ chromosomes coordinates.
<br /><br /><h4>Plots of patchwork.copynumbers()</h4>
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