Color legend for attributes track

[apurva hegde]

Hi,

I've been using IGV to visualize a bunch of samples with CNA data. I was successfully able to input my custom attributes file containing tumor type information. However, IGV seems to be assigning random colors to each of the tumor types. I was hoping to either 1) get help with figuring out the color legend indicating what color corresponds to what tumor type from my attributes file or 2) help with inserting my own attribute colors file so I can control exactly which tumor type gets what color. I've tried following these instructions: "http://software.broadinstitute.org/software/igv/SampleInformation" (bottom of the page, "Attribute Colors" section), but it doesn't tell me what to do if I have tumor type information for each sample and I want to assign a distinct color to each tumor type. It only gives information about what to do with a range of numerical values, for example. I can't seem to find any other straightforward explanation anywhere.

I've attached an example of what I have right now as a reference.
Any help is much appreciated.

[Helga Thorvaldsdottir]

Hi,

(1) To see which color corresponds to which tumor type, mouse over the color in the attribute panel and it will tell you the tumor type it corresponds to. That might be easier to do if you first sort the samples by tumor type (click on the attribute column label at the top).

(2) To control the colors, add the following lines to your attributes file (assuming the tumor type values are strings and not numbers):

#colors
<name of attribute> <attribute value 1> <color 1>

<name of attribute> <attribute value 2> <color 2>

Note that the #colors line is essential.

Colors are defined in the red,green,blue color space where each value is between 0 and 255.

Here's an example file that has two attributes named Subtype and GENDER.  Subtype has 4 different attribute values (Classical, Neural, Proneural, Mesenchymal), GENDER has 2 different attribute values (MALE, FEMALE). 

#sampleTable
Linking_id	Subtype	GENDER
TCGA-02-0001	Classical	FEMALE
TCGA-02-0002	Neural	MALE
TCGA-02-0003	Proneural	MALE
TCGA-02-0004	Mesenchymal	MALE
TCGA-02-0006	Mesenchymal	FEMALE
TCGA-02-0010	Neural	MALE
TCGA-02-0012	Proneural	MALE
#colors
Subtype	Classical	255,0,0
Subtype	Neural	0,255,0
Subtype	Proneural	110,35,180
Subtype	Mesenchymal	50,75,120
GENDER	MALE	0,0,155
GENDER	FEMALE	70,150,70

If that doesn't work for you, feel free to send us your files to igv-team at broadinstitute.org and we can take a look (ignore the auto reply that asks you to contact us at the help forum).

Helga