Example conf file for histogram and line plot

[sharvari gujja]

Hi,

Is there an example conf file for plotting histogram and line plot for figure 5 in the paper?

http://genome.cshlp.org/content/early/2009/06/15/gr.092759.109.full.pdf+html

Thanks

Sharvari

[sharvari gujja]

Hi,

I get an error trying to generate the plot:

CONFIGURATION FILE ERROR

  Configuration parameter [ticks] in parent block [_root] has been defined more

  than once in the block shown above, and has been interpreted as a list. This

  is not allowed. Did you forget to comment out an old value of the parameter?

  If you are having trouble debugging this error, first read the best practices

  tutorial for helpful tips that address many common problems

      http://www.circos.ca/documentation/tutorials/reference/best_practices

  The debugging facility is helpful to figure out what's happening under the

  hood

      http://www.circos.ca/documentation/tutorials/configuration/debugging

  If you're still stumped, get support in the Circos Google Group

      http://groups.google.com/group/circos-data-visualization

  Stack trace:

 at /home/sg15w/tools/circos-0.67-7/bin/../lib/Circos/Error.pm line 418.

Circos::Error::fatal_error('configuration', 'multivalue', 'ticks', '_root') called at /home/sg15w/tools/circos-0.67-7/bin/../lib/Circos/Configuration.pm line 441

Circos::Configuration::check_multivalues('HASH(0x2689988)', undef) called at /home/sg15w/tools/circos-0.67-7/bin/../lib/Circos/Configuration.pm line 294

Circos::Configuration::populateconfiguration('configfile', 'etc/zv9.conf', 'debug_group', 'output,summary') called at /home/sg15w/tools/circos-0.67-7/bin/../lib/Circos.pm line 146

Circos::run('Circos', 'configfile', 'etc/zv9.conf') called at ../bin/circos line 382

I have the zv9.conf file in etc/ directory.

Could you please help with this error.

Thanks

Sharvari

[Martin Krzywinski]

You have two calls to <<include ticks.conf>>.

Here are some examples of histograms in the tutorials

http://www.circos.ca/documentation/tutorials/2d_tracks/histograms/lesson

http://www.circos.ca/documentation/tutorials/2d_tracks/stacking_tracks/

http://www.circos.ca/documentation/tutorials/recipes/complex_histograms/images

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[sharvari gujja]

Hello Martin,

I still get en error after removing the duplicate call to <<include ticks.conf>>

Configuration parameter [ticks] in parent block [_root] has been defined more

  than once in the block shown above, and has been interpreted as a list. This

  is not allowed. Did you forget to comment out an old value of the parameter?

  If you are having trouble debugging this error, first read the best practices

  tutorial for helpful tips that address many common problems

      http://www.circos.ca/documentation/tutorials/reference/best_practices

  The debugging facility is helpful to figure out what's happening under the

  hood

      http://www.circos.ca/documentation/tutorials/configuration/debugging

  If you're still stumped, get support in the Circos Google Group

      http://groups.google.com/group/circos-data-visualization

  Stack trace:

 at /home/sg15w/tools/circos-0.67-7/bin/../lib/Circos/Error.pm line 418.

Circos::Error::fatal_error('configuration', 'multivalue', 'ticks', '_root') called at /home/sg15w/tools/circos-0.67-7/bin/../lib/Circos/Configuration.pm line 441

Circos::Configuration::check_multivalues('HASH(0x264aa38)', undef) called at /home/sg15w/tools/circos-0.67-7/bin/../lib/Circos/Configuration.pm line 294

Circos::Configuration::populateconfiguration('debug_group', 'output,summary', 'configfile', 'etc/zv9.conf') called at /home/sg15w/tools/circos-0.67-7/bin/../lib/Circos.pm line 146

Circos::run('Circos', 'configfile', 'etc/zv9.conf') called at ../bin/circos line 382

Attached is the conf file and 2 input files - freq.txt and qvalue.txt - both files have values for amplification and deletion.

freq.txt - histogram for amplification and deletion values

qvalue.txt - line plot for amplification and deletion values.

Appreciate all the help.

Thanks

Sharvari

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[sharvari gujja]

Hello Martin,

Using the configuration file for complex histograms for freq.txt file I get:

*** CIRCOS ERROR ***

  The field [options] did not have the expected format. The value [6.6666665]

  was expected to be a [variable value pair (x=y)]. This was seen in file

  [/home/sg15w/tools/circos-0.67-7/example/freq.txt] on line

  zv1 30149 650521 0 6.6666665

Could you please advice how to fix this error?

Thanks

Sharvari

On Tuesday, October 20, 2015 at 2:51:09 PM UTC-4, Martin wrote:

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[Martin Krzywinski]

> Configuration parameter [ticks] in parent block [_root] has been defined more

You've included ticks.conf twice.

> zv1 30149 650521 0 6.6666665

Your data file has five fields. The format for a histogram is four fields with an optional fifth options field.

http://www.circos.ca/documentation/tutorials/configuration/data_files/

Martin Krzywinski

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[sharvari gujja]

The columns in my input file are:

ChrName

Start

Stop

AmpPercentPenetrance

DelPercentPenetrance

AmpQvalue

DelQvalue

So, to get a plot similar to attached ppt or figure 5 in:

http://genome.cshlp.org/content/early/2009/06/15/gr.092759.109.full.pdf+html

Do I have to split the file into 4 tables - 2 for histograms and 2 for line plots?

I've also tried to generate a simple histogram with 4 columns, the plot doesn't look right.

Thanks for helping.

Sharvari

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[Martin Krzywinski]

I would remove the <backgrounds> and <axes> blocks from the configuration file at this stage.

Each track requires its own data file -- you'll need separate files for the histograms and line plots. There's a way around this but it gets into unnecessary detail.

Martin Krzywinski

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[sharvari gujja]

Hello Martin,

I removed <backgrounds> and <axes> blocks and have separate histogram file for the second one. The plot is not similar to Figure 5 in 

http://genome.cshlp.org/content/early/2009/06/15/gr.092759.109.full.pdf+html

Could you please let me know if I missed something here. Do I remove negative sign in 'freq3.txt' ?

Thanks

Sharvari

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[sharvari gujja]

Hello Martin,

I seem to have better histograms for amplification and deletion frequencies, but it's not similar to the excepted plot.

Could you please advice what additional parameters to tweak?

Thanks

Sharvari

[Martin Krzywinski]

Both of your histograms occupy the same r0/r1 range.

In the figure you wish to create, they do not -- they share a common baseline. What you want is something like

<plot>

r0 = 0.6r

r1 = 0.8r

...

</plot>

<plot>

r1 = 0.6r

r0 = 0.4r

...

</plot>

to make the tracks abut. 

Be careful when you're mixing 'orientation' and data with negative values. 

The orientation parameter determines the directions that positively-valued bins point.

M

Martin Krzywinski

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http://mkweb.bcgsc.ca

Sharvari

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[sharvari gujja]

I've adjusted the baselines, but the histograms are still apart..

Also, how do I set the baseline to add line plots to amplification and deletion histograms:

<plot>

type      = line

thickness = 2

max_gap = 1u

file    = ampq.txt

color   = vdred

min     = 0

max     = 0.015

r0      = 0.5r

r1      = 0.8r

</plot>

Thanks for the all the help.

Sharvari

Sharvari

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[Martin Krzywinski]

Please double check your min/max values, whether the data are positive or negative and the orientation parameter.

All of these influence the direction of the bins.

I suggest that you play with flipping the values of these parameters to learn how they influence the plot. 

Martin Krzywinski

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http://mkweb.bcgsc.ca

Sharvari

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[sharvari gujja]

Hello Martin,

I am very close to generating the plot and I really appreciate all the help. Just need help with few minor tweaks:

1. How to I change the chromosomes names to include only numbers and bring it closer to the axis?

2. Increase the histogram size and bring it closer to the outer circle?

Many thanks

Sharvari

Sharvari

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[sharvari gujja]

Also, the frequency values appear to be rounded to the nearest 20th percentile. Is there any option I could add to keep un-rounded values?

Thanks

Sharvari

[sharvari gujja]

Hello Martin,

To minimize the white space and to get chromosomes in neutral tones ( like the configuration for: http://circos.ca/documentation/tutorials/recipes/stacked_histograms/configuration), I am trying to set the background and chromosome colors. But, the plot generated does not look any different.

Could you please advise.

Thanks

Sharvari

On Thursday, October 22, 2015 at 3:52:53 PM UTC-4, Martin wrote:

Sharvari

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[Martin Krzywinski]

Remove 

label_format     = eval(sprintf("chr%s",var(label)))

which is what is adding the "chr" before the name of the chromosome.

Change the label_radius in <ideogram> to move the label.

Change r0/r1 for the histograms <plot> block to move and widen the track.

Martin Krzywinski

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http://mkweb.bcgsc.ca

Sharvari

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[Martin Krzywinski]

I'm not sure what you mean by frequency values. The histograms show exactly the values in your data set. 

Martin Krzywinski

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Sharvari

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[Martin Krzywinski]

You can change the colors of the chromosomes to luminance-normalized values.

Their colors are defined in the last field of the karyotype file. Change the colors from

chr1

to something like

lum80chr1

which is luminance 80 version of chr1 color. Also available are lum70 and lum90 variants. See etc/colors.ucsc.conf in the distribution for details.

The reason why the ideograms in the stacked histogram example look a little toned down is because cytogenetic bands are being drawn on top of the ideograms.

Martin Krzywinski

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Sharvari

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[sharvari gujja]

Hello Martin,

My ideogram.position.conf file is:

radius           = 0.9r

thickness        = 30p

fill             = yes

fill_color       = black

stroke_thickness = 2

stroke_color     = black

and the ideogram settings are:

<ideogram>

<spacing>

default = 0.005r

break   = 0.5r

axis_break_at_edge = yes

axis_break         = yes

axis_break_style   = 2

<break_style 1>

stroke_color = black

fill_color   = blue

thickness    = 0.25r

stroke_thickness = 2

</break>

<break_style 2>

stroke_color     = black

stroke_thickness = 2

thickness        = 1.5r

</break>

</spacing>

<<include ideogram.position.conf>>

<<include ideogram.label.conf>>

<<include bands.conf>>

</ideogram>

How do I change the background to add rings in the white space like:

http://circos.ca/documentation/tutorials/recipes/stacked_histograms/images

Thanks

Sharvari

Sharvari

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[sharvari gujja]

Hello Martin,

I am trying to get the scale for the plots (not ideograms)? Is there a way to do this in Circos.

Please advice.

Thanks

Sharvari

Sharvari

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[sharvari gujja]

I've tried using:

<zooms>

<zoom>

chr    = chr1

start  = 120u

end    = 125u

scale  = 2200

smooth_distance = 0.1r

smooth_steps    = 2200

</zoom>

</zooms>

But, the scale doesn't show up.

My circos plot has values from 4 input files and I am trying to get scale for the histograms and line plots.

Appreciate all the help.

Thanks

Sharvari

[Martin Krzywinski]

No, you'll need to add the y-axis labels in yourself. By using <axes> you can set up a grid for the y-values to make this easier.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

Sharvari

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[sharvari gujja]

Hello Martin,

I am trying to get a local scale similar to the figure in:

http://circos.ca/documentation/tutorials/scaling/combining_scales/images

My current conf file has <axes> defined for all the 4 plots, but doesn't show the scale. I would like to add the scale based on the min and max values for each input or each plot type:

Ampgscore

min  = 18

max  = 1535

Delgscore

min  = 14

max  = 2130

Ampq

min     = 0.6

max     = 11

Delq

min     = 0.6

max     = 11

This is the last part I am stuck at.

Appreciate all the help.

Thanks

Sharvari

Sharvari

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[Raj]

Hello guys,

i am trying to make a histogram with my data, but I am getting error like this.

I spent lots of time to figure out the issue. Can anyone help me to fix this issue.

debuggroup summary 0.13s welcome to circos v0.67-7 16 Mar 2015 on Perl 5.010001
debuggroup summary 0.13s loading configuration from file ./circos/dynamic/1025/circos.conf
debuggroup summary 0.13s found conf file ./circos/dynamic/1025/circos.conf
debuggroup summary 0.40s debug will appear for these features: output,summary
debuggroup summary 0.40s bitmap output image ./public/1025/output_20160224232816.png
debuggroup summary 0.40s parsing karyotype and organizing ideograms
debuggroup summary 0.50s karyotype has 21 chromosomes of total size 2,654,895,239
debuggroup summary 0.51s applying global and local scaling
debuggroup summary 0.53s allocating image, colors and brushes
debuggroup summary 1.33s drawing 21 ideograms of total size 2,654,895,239
debuggroup summary 1.33s drawing highlights and ideograms
debuggroup summary 2.77s found conf file /home/weihien/circos-0.67-7/bin/../etc/tracks/histogram.conf
debuggroup summary 2.77s processing track_0 histogram /home/weihien/rails_projects/clico/public/uploads/data_track/file/4935/test1.txt

  *** CIRCOS ERROR ***

  The line

  mm1 4773206 4785739 0.841390729 mm2 4919019 4938730 -0.53097179 mm2 6188465
  6213033 0.73289617 mm1 9547948 9577970 1.243845904 mm2 10056016 10080510
  0.641288587 mm1 13624845 13660546 1.014253033 mm1 16665207 16678275
  1.591207812 mm2 19371440 19394976 1.127303405 mm2 22895522 22940266
  0.555484626 mm2 23156369 23199260 1.297133917 mm2 24974117 24975098
  -0.984795881 mm2 26389339 26397122 -0.172111973 mm2 26913383 26916530
  1.35098534 mm2 28468066 28471178 1.00865779 mm2 30400471 30415813 1.130561054
  mm2 32395896 32402739 0.978697831 mm2 32414487 32451445 0.429928497 mm2
  32682609 32704137 0.413579908 mm2 32775786 32777597 0.984050423 mm2 36036326
  36049406 0.333262198 mm2 36136389 36190647 0.591476602 mm1 36691487 36693385
  1.540049029 mm1 37871738 37877387 0.852207396 mm1 37890477 37898535 0.1450897
  mm1 42851233 42905682 1.287252059 mm2 43555329 43682715 0.629442289 mm1
  43746966 43827800 0.571537584 mm1 52163448 52233232 0.727189805 mm1 52845013
  52920986 1.159514999 mm1 53313624 53326343 0.68265318 mm1 55052770 55072701
  1.387432708 mm1 55077835 55088243 0.622773529 mm1 55088132 55091307
  1.349632675 mm1 55237177 55240058 0.07565484 mm2 55253369 55296627 1.046703131
  mm1 58586384 58595964 1.29476525 mm1 58795374 58847503 0.885769052 mm1
  63143596 63176822 1.587758578 mm1 63730614 63754655 1.059150952 mm1 65158616
  65186479 0.494418 mm1 66830839 66863277 0.540391023 mm1 67123026 67231259
  2.021043972 mm2 71271063 71367749 -0.231981154 mm1 71557150 71579631
  0.488975854 mm2 71873224 71903858 1.027763009 mm2 73908447 73911326
  1.066854747 mm1 74284930 74353694 -0.157047288 mm1 74588289 74592443
  0.714772548 mm1 74713574 74737890 0.669314277 mm2 74825803 74878431
  0.678307287 mm1 79776018 79781445 0.899979869 mm2 82943634 83008937
  0.602839191 mm2 84826997 84830213 0.946874624 mm1 87264363 87310839
  -0.310823107 mm2 90847155 90866810 0.26713469 mm2 90894634 90904827
  0.869670949 mm1 92439010 92473860 0.305544895 mm1 94020493 94028326
  1.269817248 mm2 103021075 103073513 0.841122277 mm1 106538178 106714274
  -0.899036094 mm2 110262697 110314560 1.320679386 mm2 118861954 118882909
  1.117213124 mm2 119655446 119662827 1.794227982 mm2 125247190 125258608
  0.240828317 mm2 127436215 127444565 0.902093683 mm2 127587222 127606829
  0.818186918 mm2 130279309 130284547 0.236331368 mm2 130563742 130568695
  0.290796097 mm2 132846666 132866785 1.050172834 mm1 135301532 135313778
  0.34216275 mm2 136081104 136387967 0.835912088 mm1 143739029 143749676
  -0.089790116 mm2 151590549 151632593 1.530596826 mm2 152754173 152765037
  0.845320685 mm2 156078929 156144186 0.790864665 mm1 160195215 160202170
  0.802561063 mm1 161240112 161251219 0.607373189 mm2 164053540 164071169
  -0.107148955 mm1 165461037 165481214 0.719173362 mm2 170482708 170497145
  0.830386751 mm1 171127165 171150603 0.309598148 mm1 171217802 171222514
  0.589115715 mm1 171234853 171247122 1.289441227 mm1 171275990 171281186
  0.598843921 mm1 171338008 171345646 0.534784612 mm2 174461072 174464105
  1.756612481 mm1 179528055 179546267 -0.640972493 mm1 179668210 179687189
  1.380362844 mm2 180070588 180085902 0.875210693 mm1 184786776 184811313
  -0.261751223 mm1 185284726 185329396 0.419034039 mm1 191045826 191062932
  0.666317313

  from file

  /home/weihien/rails_projects/clico/public/uploads/data_track/file/4935/test1.txt

  for a track of type [histogram] did not have the expected number of fields,
  which for this track type are

  chr start end value options

  If you are having trouble debugging this error, first read the best practices
  tutorial for helpful tips that address many common problems

      

http://www.circos.ca/documentation/tutorials/reference/best_practices

  The debugging facility is helpful to figure out what's happening under the
  hood

      http://www.circos.ca/documentation/tutorials/configuration/debugging

  If you're still stumped, get support in the Circos Google Group

      http://groups.google.com/group/circos-data-visualization

  Stack trace:

Attached my data (test1) AND karyotype mouse

Thanks for your help

Raj.