FW: help with xy plot glyph

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FW: help with xy plot glyph

Jayaraman, Pushkala


Im also sending out this email to the group for more ideas and inputs about the same subject.  



Im back on Gbrowse and needed to load some quantitative data on the track.

I have been looking for a way to load the following data into our gbrowse track but haven’t found the right method or the correct set of configurations to do so..


We have 5 different samples which were measured for pain (alongwith a control score) in certain regions in the genome.. For each position Each sample has two values PAIN and CONTROL.

Hence,  5 samples will in total have 10 features on a position.  Currently for 3 features, I am showing the data like this..


As you can see,, it is neither intuitive nor makes sense..


To show this data I would like to know if we have have a glyph that can show both the scores from all 5 samples at once at the same position. Something like this…  




While I was going through Bio::Graphics::Image, I came across this link that took me to the flybase Gbrowse which had this image



Could you help direct me to the right resources to do something similar?



Thanks for taking the time to read and understand such a complicated email (couldn’t understand it when I read it aloud to myself :P). also attached is the email that I sent to the forum with my current configurations for this track.


Pushkala Jayaraman


Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229




Im back into Gbrowse and just started with displaying quantitative data on xyplots. Ive used the xy-plot glyph before to show density plots and that used to work fine.. but with quantitative data I seem to be runnig into problems..


Here is my gff3 file (as you may see, this is data form 5 samples each of them have a control score and a pain score. For the same position. I need to create subtracks for all 8 features. 5 sample types and also ‘pain’ and ‘control’ source. But it doesn’t seem to be accepting the different sample types although, it does show them in the box, it doesn’t filter them.



Chr1       CONTROL            methylation_score_1     31897    31898    0.9752066            +             .               ID=CTRL_0;Name=CTRL

Chr1       PAIN      methylation_score_1     31897    31898    0.9781421            +             .               ID=SNL_1;Name=SNL

Chr1       CONTROL            methylation_score_2     31897    31898    0.98540145          +             .               ID=CTRL_2;Name=CTRL

Chr1       PAIN      methylation_score_2     31897    31898    0.9862069            +             .               ID=SNL_3;Name=SNL

Chr1       CONTROL            methylation_score_3     31897    31898    0.9946524            +             .               ID=CTRL_4;Name=CTRL

Chr1       PAIN      methylation_score_3     31897    31898    0.97115386          +             .               ID=SNL_5;Name=SNL

Chr1       CONTROL            methylation_score_4     31897    31898    0.990566              +             .               ID=CTRL_6;Name=CTRL

Chr1       PAIN      methylation_score_4     31897    31898    0.9622642            +             .               ID=SNL_7;Name=SNL

Chr1       CONTROL            methylation_score_5     31897    31898    0.9723757            +             .               ID=CTRL_8;Name=CTRL

Chr1       PAIN      methylation_score_5     31897    31898    0.9896373            +             .               ID=SNL_9;Name=SNL

Chr1       CONTROL            methylation_score_1     31907    31908    0.9586777            +             .               ID=CTRL_10;Name=CTRL

Chr1       PAIN      methylation_score_1     31907    31908    0.9726776            +             .               ID=SNL_11;Name=SNL

Chr1       CONTROL            methylation_score_2     31907    31908    0.98540145          +             .               ID=CTRL_12;Name=CTRL

Chr1       PAIN      methylation_score_2     31907    31908    0.9724138            +             .               ID=SNL_13;Name=SNL

Chr1       CONTROL            methylation_score_3     31907    31908    0.96256685          +             .               ID=CTRL_14;Name=CTRL

Chr1       PAIN      methylation_score_3     31907    31908    0.93333334          +             .               ID=SNL_15;Name=SNL

Chr1       CONTROL            methylation_score_4     31907    31908    0.9433962            +             .               ID=CTRL_16;Name=CTRL

Chr1       PAIN      methylation_score_4     31907    31908    0.9496855            +             .               ID=SNL_17;Name=SNL

Chr1       CONTROL            methylation_score_5     31907    31908    0.98342544          +             .               ID=CTRL_18;Name=CTRL

Chr1       PAIN      methylation_score_5     31907    31908    0.95811516          +             .               ID=SNL_19;Name=SNL



Here is my conf file..



feature        = methylation_score_1 methylation_score_2 methylation_score_3 methylation_score_4 methylation_score_5

glyph          = xyplot

graph_type     = points

fgcolor        = sub{

                                                                                my $feature = shift->source;

                                                                                return $feature eq "PAIN" ? "blue":"magenta";


bgcolor        = black

select         = source 'PAIN' 'CONTROL'

min_score    = 0

max_score    = 1

clip = 1

label = sub{

                                                my $feature = shift;

                                                my ($class)=$feature->load_id;

                                                return $class;



scale          = right

group_on  = primary_tag

category       = Quantitative Data

key            = Methylation Studies




Hence if the source is PAIN or CONTROL selected, I do not see any glyphs on the track and can only see the 5 scales..






What am I doing wrong??




Pushkala Jayaraman


Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229



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