Question: How to label gene name only for those segments with amplifications or deletions
0
gravatar for sebastianzeki0
4.4 years ago by
United Kingdom
sebastianzeki0170 wrote:

I've got about 10 tumours plotted as copy number plots (histograms) as a circos plot (using the tools from http://www.circos.ca/). I also have a file with all the gene names and when I construct the plot it's a bit much to look at and I wondered if there was a way of only labelling the genes in (preferably outside the ideogram) those segments with significantly amplified or deleted copy number plots (on any of the plots)

 

So far I have the following (only two tracks  shown for the sake of brevity) in circos.conf

 

show_histogram = yes

<<include colors_fonts_patterns.conf>>

<<include ideogram.conf>>
<<include ticks.conf>>

<image>
<<include etc/image.conf>>

file*   = compareAllWGS_FREEC.png
</image>

karyotype         = data/karyotype/karyotype.human.txt
chromosomes_units = 500000
#chromosomes       = hs1;hs2;hs3
chromosomes = -hsX;-hsY
chromosomes_display_default = yes

<plots>


show_grid  = yes
show = yes

<plot>

type         = histogram
file = /Users/SZ/Desktop/SequencingScripts/circos/circos-0.67-4/data/circos/0.5M/wgscircos/LP6005334-DNA_A03.bam_ratio.txt.CIRCOS.txt
thickness    = 2
color        = green
fill_under   = yes
fill_color   = green
r0           = 0.05r
r1           = 0.1r
max_gap      = 20u
min          = 0
max = 8
z = 10
<rules>

<rule>
condition = var(value) > 3
fill_color   = black
show = yes
</rule>

<rule>
condition = var(value) < 1.6
fill_color   = red
show = yes
z = 10
</rule>

</rules>
</plot>

<plot>

type         = histogram
file = /Users/SZ/Desktop/SequencingScripts/circos/circos-0.67-4/data/circos/0.5M/wgscircos/LP6005334-DNA_D01.bam_ratio.txt.CIRCOS.txt
orientation  = out
thickness    = 1
color        = green
fill_under   = yes
fill_color   = green
r0           = 0.1r
r1           = 0.15r
max_gap      = 20u
min          = 0
max = 8
z = 10
<rules>

<rule>
condition = var(value) > 3
fill_color   = black
show = yes
</rule>
<rule>
condition = var(value) < 1.6
fill_color   = red
show = yes
z = 10
</rule>

</rules>
</plot>

<plot>
type             = text
color            = black
file             = /Users/SZDesktop/SequencingScripts/bedtools/bedtools2-master/LP6005334-DNA_A03.bed
r1   = 1r+300p
r0   = 1r
label_size = 8p
show_links     = yes
link_dims      = 1p,1p,2p,1p,1p
link_thickness = 1p
link_color     = red
padding        = 2p
rpadding       = 2p
label_snuggle         = yes
max_snuggle_distance  = 10r
snuggle_tolerance     = 0.25r
snuggle_sampling      = 2
</plot>
</plots>

<<include etc/housekeeping.conf>>
data_out_of_range* = trim
circos copy number plots • 2.2k views
ADD COMMENTlink modified 4.4 years ago by RamRS21k • written 4.4 years ago by sebastianzeki0170
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