Text Label In Circos

Question

[dustar1986]

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.

[Josh Herr]

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

[dustar1986]

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.

[Josh Herr]

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.

[dustar1986]

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

[dustar1986]

Circos Google Group helps! A lot of thanks!

Answer 1

[dustar1986]

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.

Answer 2

[Sandeep]

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.

[dustar1986]

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.