Issue with background colour and contig colours

[Sutrisha Kundu]

Hi, 

I was trying to do a circos plot for my plant genome file with karyotype.txt and genedensity.txt. On running the files, I get an image with completely different background and contig colours, different from what i mentioned in the config file as attached below:

Circos1.conf file

<<include etc/housekeeping.conf>>

<colors>
  red         = #FF0000
  green       = #00FF00
  blue        = #0000FF
  yellow      = #FFFF00
  magenta     = #8B008B
  black       = #000000
  orange      = #FFA500
  pink        = #FFC0CB
  brown       = #A52A2A
  violet      = #EE82EE
  cyan        = #00FFFF
  darkgreen   = #006400
  lightpink   = #FFB6C1
  turquoise   = #40E0D0
  olive       = #808000
  lime        = #00FF00
  slateblue   = #6A5ACD
  white       = #FFFFFF
  white_a0 = white
  black_a0 = black
</colors>

<fonts>
  default = /usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
</fonts>

karyotype = Bamboo_circos/fixed_karyotype.txt

<ideogram>
  radius     = 0.8r
  thickness  = 30p
  fill       = yes
  show       = yes
  <spacing>
    default = 0.01r
  </spacing>
  <label>
    show  = yes
    font  = default
    size  = 20p
    color = black # Set ideogram label color explicitly to black
  </label>
  <ticks>
    show       = yes
    multiplier = 1e-6
    color      = black
    size       = 12p
    format     = %.1f
    thickness  = 1p
    <label>
      font  = bold
      size  = 14p
      color = black
      show  = yes
    </label>
  </ticks>
</ideogram>

<plots>
  <plot>
    type       = histogram
    file       = Bamboo_circos/density.txt
    r0         = 0.75r
    r1         = 0.95r
    color      = red
    fill       = yes  # Explicitly define fill
    stroke     = black  # Explicitly define stroke color
    thickness  = 2
    fill_under = yes
  </plot>
</plots>

<image>
  dir     = .
  file    = circos_plot.png
  png     = yes
  svg     = yes
  radius  = 1500p
  <background>
    color     = white
    opacity   = 1
  </background>
</image>

#karyotype.txt file

chr1 - Btu01A.ctg01 Btu01A.ctg01 0 63258871 red
chr2 - Btu01B.ctg04 Btu01B.ctg04 0 53411334 red
chr3 - Btu01B.ctg30 Btu01B.ctg30 0 25813907 red
chr4 - Btu01C.ctg11 Btu01C.ctg11 0 39878854 red
chr5 - Btu02A.ctg07 Btu02A.ctg07 0 47044180 green
chr6 - Btu02B.ctg06 Btu02B.ctg06 0 49379162 green
chr7 - Btu02C.ctg22 Btu02C.ctg22 0 28855024 green
chr8 - Btu03A.ctg05 Btu03A.ctg05 0 52669080 blue
chr9 - Btu03B.ctg03 Btu03B.ctg03 0 54687919 blue
chr10 - Btu03C.ctg16 Btu03C.ctg16 0 34814095 blue
chr11 - Btu04A.ctg09 Btu04A.ctg09 0 41514731 yellow
chr12 - Btu04B.ctg32 Btu04B.ctg32 0 23765677 yellow
chr13 - Btu04C.ctg33 Btu04C.ctg33 0 22410140 yellow
chr14 - Btu05A.ctg34 Btu05A.ctg34 0 22088693 magenta
chr15 - Btu05A.ctg39 Btu05A.ctg39 0 13801444 magenta
chr16 - Btu05B.07C.ctg02 Btu05B.07C.ctg02 0 63166063 black
chr17 - Btu05C.ctg27 Btu05C.ctg27 0 27312430 magenta
chr18 - Btu06A.ctg08 Btu06A.ctg08 0 42054038 orange
chr19 - Btu06B.ctg12 Btu06B.ctg12 0 39525444 orange
chr20 - Btu06C.ctg13 Btu06C.ctg13 0 38038513 orange
chr21 - Btu07A.ctg19 Btu07A.ctg19 0 31343864 pink
chr22 - Btu07B.ctg17 Btu07B.ctg17 0 33380477 pink
chr23 - Btu08A.ctg20 Btu08A.ctg20 0 30616773 brown
chr24 - Btu08A.ctg43 Btu08A.ctg43 0 10472293 brown
chr25 - Btu08B.ctg14 Btu08B.ctg14 0 36580926 brown
chr26 - Btu08C.ctg21 Btu08C.ctg21 0 30414204 brown
chr27 - Btu09A.ctg26 Btu09A.ctg26 0 27364476 violet
chr28 - Btu09B.ctg31 Btu09B.ctg31 0 23906781 violet
chr29 - Btu09C.ctg18 Btu09C.ctg18 0 32100134 violet
chr30 - Btu10A.ctg29 Btu10A.ctg29 0 26406508 cyan
chr31 - Btu10B.ctg28 Btu10B.ctg28 0 26828703 cyan
chr32 - Btu10C.ctg25 Btu10C.ctg25 0 27748238 cyan
chr33 - Btu11A.ctg10 Btu11A.ctg10 0 40653237 darkgreen
chr34 - Btu11A.ctg35 Btu11A.ctg35 0 20034937 darkgreen
chr35 - Btu11B.ctg36 Btu11B.ctg36 0 18583396 darkgreen
chr36 - Btu11B.ctg42 Btu11B.ctg42 0 11242639 darkgreen
chr37 - Btu11C.ctg24 Btu11C.ctg24 0 27893588 darkgreen
chr38 - Btu12A.ctg23 Btu12A.ctg23 0 29269768 lightpink
chr39 - Btu12B.ctg15 Btu12B.ctg15 0 35674677 lightpink
chr40 - Btu.ctg37 Btu.ctg37 0 16353879 turquoise
chr41 - Btu.ctg38 Btu.ctg38 0 15217677 olive
chr42 - Btu.ctg40 Btu.ctg40 0 12491141 lime
chr43 - Btu.ctg41 Btu.ctg41 0 12004685 slateblue

#small snippet of density.txt file

Btu01A.ctg01 0 100000 0.0
Btu01A.ctg01 100000 200000 0.0
Btu01A.ctg01 200000 300000 0.0
Btu01A.ctg01 300000 400000 0.0
Btu01A.ctg01 400000 500000 0.0
Btu01A.ctg01 500000 600000 7.0
Btu01A.ctg01 600000 700000 6.0
Btu01A.ctg01 700000 800000 10.0
Btu01A.ctg01 800000 900000 8.0
Btu01A.ctg01 900000 1000000 8.0
Btu01A.ctg01 1000000 1100000 3.0
Btu01A.ctg01 1100000 1200000 9.0
Btu01A.ctg01 1200000 1300000 7.0

Please help me where I am going wrong?

I have also attached the image output obtained.