Dot size adjustment possible when using display as Point?

[Jasper HTU]

Hi,

I want to display several SNP arrays along WES data and am using the .CN format for loading Lg2 ratio and BAF/heterozygosity (range 0 to 1) for the same sample at the same time. At the moment I adjust track height, Y-as range and data type to Point mannualy and will generate a track display line. However I did not find an option for increasing the dot size from default. While using GWAS data dot size is dependent on p-value. I can't mis-use/re-use the GWAS format as Lg2ratio also goes down for 'deletion regions'. Did I miss some line of information or is it not included in IGV (2.3.90)? Should I go to IGV Light? However I am not really a coder.

At last, but not the least: Thx for IGV!

Jasper Saris

Dept Clinical Genetics, Erasmus MC

[Jim Robinson]

Hi Jasper,

You didn't miss anything, it is not there for .cn files unfortunately.   That is an oversight, I look into a fix.   If you could attach a small sample file of a .CN file with representative data that would be helpful.    I am not quite following the "down for 'deletion regions'" comment but its been a long time since I dealt with the GWAS format.   Some sample data should make it clear.

Jim

[Jasper HTU]

Hi Jim,

Attached is a .cn file with SNP array data of part of chromosome 1 and a corresponding view in IGV of the region. Per sample I import the Lg2R and BAF, and change the color for positive Lg2R into red. Regarding the 'down for deletion regions'; With Lg2R we have also negative values/points, which does not fit with the always positive p-values for GWAS and the GWAS file format.

Jasper

Op woensdag 25 januari 2017 16:48:40 UTC+1 schreef Jim Robinson:

[Jim Robinson]

Hi, just getting back to this.  To be clear,  do you want to increase the dot size uniformly, or make it proportional to the value?  

[Jasper HTU]

Hi, 

Sorry, I missed your answer. For now, increasing dot size uniformly was the main reason. 

An option to make it proportional would be a bonus (which clearly makes it possible to detect/spot outliers and, more importantly, reduces cluttering around zero). The size should that be limited also at the extremes, e.g. in a homozygous loss the Log2R drops to very large negative vaules. And double null-genotypes would also generate large dots. So for me, I would be happy with a uniform increase/setting.

Jasper

2017-02-07 1:13 GMT+01:00 Jim Robinson <jrob...@broadinstitute.org>:

Hi, just getting back to this.  To be clear,  do you want to increase the dot size uniformly, or make it proportional to the value?  

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[Luca Tosti]

Dear Jim,

Is it possible to achieve what Jasper had asked?

Thank you!

On Tuesday, February 14, 2017 at 3:17:36 PM UTC Jasper HTU wrote:

Hi, 

Sorry, I missed your answer. For now, increasing dot size uniformly was the main reason. 

An option to make it proportional would be a bonus (which clearly makes it possible to detect/spot outliers and, more importantly, reduces cluttering around zero). The size should that be limited also at the extremes, e.g. in a homozygous loss the Log2R drops to very large negative vaules. And double null-genotypes would also generate large dots. So for me, I would be happy with a uniform increase/setting.

Jasper

2017-02-07 1:13 GMT+01:00 Jim Robinson <jrob...@broadinstitute.org>:

Hi, just getting back to this.  To be clear,  do you want to increase the dot size uniformly, or make it proportional to the value?  

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[igv-help]

Unfortunately no, this looks like it did not get implemented.    I have opened an issue for this here https://github.com/igvteam/igv/issues/1438