I am trying to have a plot that shows histograms, links, and gene labels. When I add a label block to my config file and run my config file, the histogram does not show, only the links and label show on the plot, but without the label block, the histogram and links show in the plot.
I have attached a copy of my configuration file and the plots I get each time. I would appreciate any suggestion on how to have all the same figure.
# circos.conf
# usuage: circos -conf ./test.conf -noparanoid
karyotype = /apps/circos/0.69-9/data/karyotype/karyotype.human.hg38.txt
chromosomes_units = 1000000
##############################
#Histogram plot
<plots>
<plot>
type = histogram
file = /120k_hs.txt
r1 = 0.95r
r0 = 0.7r
fill_color = vdgrey
extend_bin = no
#<rules>
#<rules>
#<<include exclude.hs1.rule>>
#</rules>
</plot>
</plots>
#################################
#link configuration
<links>
<link>
file = /genic_hs.txt
radius = 0.7r
bezier_radius = 0.1r
color = black_a4
thickness = 2
<rules>
<rule>
condition = var(intrachr)
show = yes
</rule>
<rule>
condition = 1
color = eval(var(chr2))
flow = continue
</rule>
<rule>
condition = from(hs1)
radius1 = 0.7r
</rule>
<rule>
condition = to(hs1)
radius2 = 0.7r
</rule>
</rules>
</link>
</links>
#################################
#################################
#Gene labels
<plots>
<plot>
type = text
file = /TSG_Oncogene.txt
r1 = 1r+200p
r0 = 1r
label_font = condensed
label_size = 24p
rpadding = 0p
padding
= 0p
show_links = yes
link_dims = 0p,0p,60p,0p,10p
link_thickness = 2p
link_color = black
</ploIt>
</plots>
#################################
#ideogram configuration
<ideogram>
<spacing>
default = 0.005r
</spacing>
# Ideogram position, fill and outline
radius = 0.90r
thickness = 20p
fill = yes
stroke_color = dgrey
stroke_thickness = 2p
# Minimum definition for ideogram labels.
show_label = yes
# see etc/fonts.conf for list of font names
label_font = default
label_radius = 1r + 75p
label_size = 30
label_parallel = yes
</ideogram>
############################################
#ticks configuration
show_ticks = yes
show_tick_labels = yes
<ticks>
radius = 1r
color = black
thickness = 2p
# the tick label is derived by multiplying the tick position
# by 'multiplier' and casting it in 'format':
#
# sprintf(format,position*multiplier)
#
multiplier = 1e-6
# %d - integer
# %f - float
# %.1f - float with one decimal
# %.2f - float with two decimals
#
# for other formats, see
http://perldoc.perl.org/functions/sprintf.html format = %d
<tick>
spacing = 5u
size = 10p
</tick>
<tick>
spacing = 25u
size = 15p
show_label = yes
label_size = 20p
label_offset = 10p
format = %d
</tick>
</ticks>
############################################
## The remaining content is standard and required. It is imported
# from default files in the Circos distribution.
#
# These should be present in every Circos configuration file and
# overridden as required. To see the content of these files,
# look in etc/ in the Circos distribution
<image>
# Included from Circos distribution.
dir = .
file =intgn.png
png = yes
radius = 2500p
</image>
# RGB/HSV color definitions, color lists, location of fonts, fill patterns.
# Included from Circos distribution.
<<include /apps/circos/0.69-9/etc/colors_fonts_patterns.conf>>
# Debugging, I/O an dother system parameters
# Included from Circos distribution.
<<include /apps/circos/0.69-9/etc/housekeeping.conf>>