Question: Text Label In Circos
0
gravatar for dustar1986
6.2 years ago by
dustar1986290
USA
dustar1986290 wrote:

Hi,

I'm using Circos 0.62 to build up ideomgram. But I found that text label never showed (and "-debuggroup textplace" always returns "not_place" ).

My conf file is like following:

<colors>
<<include A_PATH_TO_FILE/circos-0.62/etc/colors.conf>>
<<include A_PATH_TO_FILE/circos-0.62/etc/brewer.conf>>
</colors>
<fonts>
<<includeA_PATH_TO_FILE/circos-0.62/etc/fonts.conf>>
</fonts>
<<includeA_PATH_TO_FILE/conf/ideogram.conf>>
<<include A_PATH_TO_FILE/conf/ticks.conf>>
<image>
<<include A_PATH_TO_FILE/circos-0.62/etc/image.conf>>
</image>
karyotype =A_PATH_TO_FILE/karyo.txt
chromosomes_units = 1
chromosomes_display_default =  no
chromosomes = chr18
<plots>
<plot>
type=heatmap
file = A_PATH_TO_FILE/ref.txt
color = spectral-9-div-rev
stroke_thickness = 1
stroke_color     = black
r0= 0.925r
r1= 0.925r-15p
</plot>
<plot>
type=heatmap
file = A_PATH_TO_FILE/heatmap1.txt
color = spectral-9-div-rev
stroke_thickness = 1
stroke_color     = black
r0= 1.15r
r1= 1.15r+15p
</plot>
<plot>
type=text
color=black
file = A_PATH_TO_FILE/name1.txt
r0= 1.15r+20p
r1= 1.15r+40p
label_size=16p
label_parallel=yes
label_font=condensed
padding=0p
rpadding=0p
</plot>
</plots>
<<include A_PATH_TO_FILE/circos-0.62/etc/housekeeping.conf>>

And ideogram radius is set to 0.4r and the size of the image inscribed is 1500p.

In the output everything is fine except the missing text label.

My "ref.txt":

chr18    43316154    43316237    100    color=yellow    +

My "heatmap1.txt":

chr18    43315154    43317237    100    color=purple    +

My "name1.txt":

chr18    43315154    43317237    uc008eue.1

Does anyone use Circos and know what's wrong with my settings?

Thank you very much.

• 3.3k views
ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by dustar1986290

Are you getting an error message? My initial assumption would be that the text data is somehow not being written to the figure.

ADD REPLYlink written 6.2 years ago by Josh Herr5.6k

Yes. The message is something like " debuggroup summary 2.59s placing text track PATH_TO_FILE/name1.txt
debuggroup textplace 2.65s not_placed chr18 43315154 43317237 uc008eue.1 " The graph will be created with text label missing. The other graph elements are there as expected.

ADD REPLYlink written 6.2 years ago by dustar1986290

Hmmm... I don't know. I don't have a ton of experience with Circos, so I can't help out here on this error. Trial and error fixing (like I do with HTML, CSS, and JavaScript for webpages) might be something to try. I assume you consulted the Circos Google Group? It's the best place for help.

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by Josh Herr5.6k

Thanks for the suggestion, Josh. I'll try.

ADD REPLYlink written 6.2 years ago by dustar1986290

Circos Google Group helps! A lot of thanks!

ADD REPLYlink written 6.2 years ago by dustar1986290
2
gravatar for dustar1986
6.2 years ago by
dustar1986290
USA
dustar1986290 wrote:

Finally, as @Josh Herr suggestion I searched Circos Google Group.

In the <plot> block for text label, the "r1" value should be larger enough than "r0", saying 200p larger. This will give enough space to show the text.

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by dustar1986290
1
gravatar for Sandeep
6.2 years ago by
Sandeep250
Manipal, India
Sandeep250 wrote:

I would suggest to look into the ideogram.label.conf file. There is a 'show_label' option, you can choose to have a 'yes' or a 'no' there.

Also the label for ticks can be shown by changing the ticks.confg file by changing the show_tick_labels=yes.

ADD COMMENTlink written 6.2 years ago by Sandeep250

Thank Sandeep. However, I think "show_label" is the option to show the label of ideogram itself (say, chr1, chr2 etc). "show_tick_labels" is the option to show ideogram scale. That seems not what I want. Thanks again for the kind reply.

ADD REPLYlink written 6.2 years ago by dustar1986290
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