missing histogram plot

[Ibk]

Hi,

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.

Thanks

Ibk

my_cofig.conf

# 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>>