Loop track colours

[Helen Long]

Hi, 

I am uploading custom long range text tracks into the browser. I am wondering if there is a way to change the colour of a subset of the loops. I would like to spotlight particular loops for a figure. Thank you for your help. 

Best wishes, 

Helen 

[lid...@gmail.com]

Hi Helen,

technically yes, while the trick part is how to define the subset? by score range?

if you want to highlight just a few of arcs, you can download the plot as svg from screenshot app, then edit in illustrator or inkscape (or any other vector image editing software)

or you can add an additional column (with color, can use name or hex code) to your data, I can quickly develop a patch for this feature.

Thanks!

[Helen Long]

Hi, 

Thanks for your help! I am selecting the loops by overlap with particular features so it would be easy for me to add another column, if it would be possible to have a hex code column that would be amazing. Otherwise I will have a go at doing it in illustrator. 

Best wishes, 

Helen 

[lid...@gmail.com]

Sure, I can implement that feature, please send me your example file when you get it. I will let you know once it's done.

Thanks!

[Helen Long]

Hi, 

Thanks so much! I have created the below example to show how my file would look. These loops are on hg19. It adds a feature column and a hex code column to the long range text track format, if the "Feature" column is a problem it could be omitted.

chr1        36612957        36628346        chr1:36746973-36748711,10.92        FeatureA        A7226E  
chr1        36746973        36748711        chr1:36612957-36628346,10.92        FeatureA        A7226E  
chr1        36612957        36628346        chr1:36748712-36749060,7.1        FeatureA        A7226E  
chr1        36748712        36749060        chr1:36612957-36628346,7.1        FeatureA        A7226E  
chr1        36612957        36628346        chr1:36749061-36751369,11.12        FeatureB        EC2049
chr1        36749061        36751369        chr1:36612957-36628346,11.12        FeatureB        EC2049
chr1        36612957        36628346        chr1:36751370-36753679,8.72        FeatureB        EC2049
chr1        36751370        36753679        chr1:36612957-36628346,8.72        FeatureB        EC2049
chr1        36612957        36628346        chr1:36753680-36755468,5.44        FeatureB        EC2049
chr1        36753680        36755468        chr1:36612957-36628346,5.44        FeatureB        EC2049
chr1        36612957        36628346        chr1:36757650-36760097,8.19        FeatureC        F26B38 
chr1        36757650        36760097        chr1:36612957-36628346,8.19        FeatureC        F26B38 
chr1        36612957        36628346        chr1:36760098-36762047,8.25        FeatureC        F26B38 
chr1        36760098        36762047        chr1:36612957-36628346,8.25        FeatureC        F26B38 
chr1        36612957        36628346        chr1:36762048-36763430,5.68        FeatureD        F7DB4F
chr1        36762048        36763430        chr1:36612957-36628346,5.68        FeatureD        F7DB4F
chr1        36612957        36628346        chr1:36768997-36771650,5.9        FeatureD        F7DB4F
chr1        36768997        36771650        chr1:36612957-36628346,5.9        FeatureD        F7DB4F
chr1        36612957        36628346        chr1:36848555-36852470,5.76        FeatureE        355C7D
chr1        36848555        36852470        chr1:36612957-36628346,5.76        FeatureE        355C7D
chr1        36612957        36628346        chr1:36858888-36863901,5.61        FeatureE        355C7D
chr1        36858888        36863901        chr1:36612957-36628346,5.61        FeatureE        355C7D
chr1        36612957        36628346        chr1:36883305-36888534,8.18        FeatureF        A8A7A7
chr1        36883305        36888534        chr1:36612957-36628346,8.18        FeatureF        A8A7A7
chr1        36689675        36690929        chr1:36744673-36746972,5.09        FeatureF        A8A7A7
chr1        36744673        36746972        chr1:36689675-36690929,5.09        FeatureF        A8A7A7
chr1        36689675        36690929        chr1:36746973-36748711,5.86        FeatureG        E5FCC2
chr1        36746973        36748711        chr1:36689675-36690929,5.86        FeatureG        E5FCC2
chr1        36689675        36690929        chr1:36749061-36751369,7.81        FeatureG        E5FCC2
chr1        36749061        36751369        chr1:36689675-36690929,7.81        FeatureG        E5FCC2
chr1        36689675        36690929        chr1:36751370-36753679,6.43        FeatureH        594F4F
chr1        36751370        36753679        chr1:36689675-36690929,6.43        FeatureH        594F4F
chr1        36689675        36690929        chr1:36753680-36755468,5.53        FeatureH        594F4F
chr1        36753680        36755468        chr1:36689675-36690929,5.53        FeatureH        594F4F

Thank you for your help!

Best wishes, 

Helen

[lid...@gmail.com]

Hi Helen,

you are welcome! I will work on this and let you know.

[lid...@gmail.com]

Hi Helen,

I have added this feature, you can refresh the browser and choose the following menu when upload text track

then you should be able to see the colors for each arc, also the name/feature in the tooltip

please note I added a `#` in the color column for future support with rgb(x,x,x) or names like red etc, that make things easier.

also attached the modified file which shows the screenshot above.

Feel free to let me know any issue.

Thanks!

[lid...@gmail.com]

sorry forgot the file.

[Helen Long]

Amazing! Thank you so much for your help, I really appreciate it!

Best wishes, 

Helen