Entering edit mode
9.9 years ago
sebastianzeki0
▴
240
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