<<include colors_fonts_patterns.conf>>

<<include etc/housekeeping.conf>>

<<include Candida_albicans_SC5314.chrM.ideogram.conf>>
<<include Candida_albicans_SC5314.chrM.ticks.conf>>

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

karyotype   = Candida_albicans_SC5314.chrM.karyotype

chromosomes_units           = 10
chromosomes_display_default = no
chromosomes                 = chrM

<plots>

type      = histogram
thickness = 2

<plot>
show    = yes
file    = /woldlab/castor/data00/home/georgi/genomes/Candida/Candida_albicans_SC5314/mappability/Candida_albicans_SC5314.36mers.Candida_albicans_SC5314.bowtie.mappability.unique.chrM.wig
z       = 5
max_gap = 0u
fill_under = yes
fill_color = dred
color   = dred
min     = 0
max     = 36
r0      = 0.93r
r1      = 0.98r
</plot>

<plot>
show    = yes
file    = /woldlab/castor/data00/home/georgi/genomes/Candida/Candida_albicans_SC5314/mappability/Candida_albicans_SC5314.36mers.chrM-vs-chrM.bowtie.k3m2.mappability.unique.wig
z       = 5
max_gap = 0u
fill_under = yes
fill_color = ylorrd-9-seq-2
color   = black
min     = 0
max     = 36
r0      = 0.88r
r1      = 0.93r
</plot>

# <plot>
# type = tile
# file = Arabidopsis_thaliana.TAIR10.19.fixed.chrM.gff3.protein_coding_gene.plus.tile
# layers = 2
# layers_overflow = hide
# margin = 0.2u
# thickness = 12
# padding = 6
# orientation = out
# stroke_thickness = 1
# stroke_color = green
# color = green
# r0 = 0.76r
# r1 = 0.78r
# </plot>

# <plot>
# type = tile
# file = Arabidopsis_thaliana.TAIR10.19.fixed.chrM.gff3.protein_coding_gene.minus.tile
# layers = 2
# layers_overflow = hide
# margin = 0.2u
# thickness = 12
# padding = 6
# orientation = out
# stroke_thickness = 1
# stroke_color = orange
# color = orange
# r0 = 0.74r
# r1 = 0.76r
# </plot>

# <plot>
# type = tile
# file = Arabidopsis_thaliana.TAIR10.19.fixed.chrM.gff3.repeat.tiles
# layers = 2
# layers_overflow = hide
# margin = 0.2u
# thickness = 12
# padding = 6
# orientation = out
# stroke_thickness = 1
# stroke_color = red
# color = red
# r0 = 0.70r
# r1 = 0.74r
# </plot>

# <plot>
# type = tile
# file = Arabidopsis_thaliana.TAIR10.19.fixed.chrM.gff3.rRNA.minus.tiles
# layers = 2
# layers_overflow = hide
# margin = 0.2u
# thickness = 12
# padding = 6
# orientation = out
# stroke_thickness = 1
# stroke_color = blue
# color = blue
# r0 = 0.68r
# r1 = 0.70r
# </plot>

# <plot>
# type = tile
# file = Arabidopsis_thaliana.TAIR10.19.fixed.chrM.gff3.tRNA_gene.plus.tiles
# layers = 2
# layers_overflow = hide
# margin = 0.2u
# thickness = 12
# padding = 6
# orientation = out
# stroke_thickness = 1
# stroke_color = purple
# color = purple
# r0 = 0.66r
# r1 = 0.68r
# </plot>

# <plot>
# type = tile
# file = Arabidopsis_thaliana.TAIR10.19.fixed.chrM.gff3.tRNA_gene.minus.tiles
# layers = 2
# layers_overflow = hide
# margin = 0.2u
# thickness = 12
# padding = 6
# orientation = out
# stroke_thickness = 1
# stroke_color = grey
# color = grey
# r0 = 0.64r
# r1 = 0.66r
# </plot>

# <plot>
# type = text
# file = ce10.chrM.protein_coding.text
# color      = black
# label_font = bold
# label_size = 36p
# label_parallel   = no
# padding = 15p
# rpadding = 15p
# z       = 1
# r0 = 1.02r
# r1 = 1.22r
# </plot>


<plot>
show    = yes
file    = 3-Candida_albicans/Hos2-9myc_hypha_ChIP_Rep1-GSM941974.chrM.32mers.k3m2.minus.RPM.wig.sign_flipped
z       = 5
max_gap = 0u
orientation = in
fill_under = yes
fill_color = ylorrd-9-seq-7
color   = ylorrd-9-seq-9
min     = 0
max     = 4510
r0      = 0.78r
r1      = 0.83r
</plot>


<plot>
show    = yes
file    = 3-Candida_albicans/Hos2-9myc_hypha_ChIP_Rep1-GSM941974.chrM.32mers.k3m2.plus.RPM.wig
z       = 5
max_gap = 0u
fill_under = yes
fill_color = ylorrd-9-seq-9
color   = ylorrd-9-seq-7
min     = 0
max     = 4292
r0      = 0.83r
r1      = 0.88r
</plot>


<plot>
show    = yes
file    = 3-Candida_albicans/Hos2-9myc_hypha_input-GSM941973.chrM.32mers.k3m2.minus.RPM.wig.sign_flipped
z       = 5
max_gap = 0u
orientation = in
fill_under = yes
fill_color = greens-9-seq-2
color   = purd-9-seq-5
min     = 0
max     = 1692
r0      = 0.68r
r1      = 0.73r
</plot>


<plot>
show    = yes
file    = 3-Candida_albicans/Hos2-9myc_hypha_input-GSM941973.chrM.32mers.k3m2.plus.RPM.wig
z       = 5
max_gap = 0u
fill_under = yes
fill_color = purd-9-seq-5
color   = greens-9-seq-2
min     = 0
max     = 1589
r0      = 0.73r
r1      = 0.78r
</plot>

</plots>
