<<include colors_fonts_patterns.conf>>

<<include etc/housekeeping.conf>>

<<include Zea_mays.chloroplast.ideogram.conf>>
<<include Zea_mays.chloroplast.ticks.conf>>

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

karyotype   = Zea_mays.chloroplast.karyotype

chromosomes_units           = 10
chromosomes_display_default = no
chromosomes                 = chrP

<plots>

type      = histogram
thickness = 2

<plot>
show    = yes
file    = mappability-Zea_mays/Zea_mays.AGPv3.36mers.Zea_mays.AGPv3.bowtie.mappability.unique.chrP.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    = organelle-genome-cross-mapping/Zea_mays.AGPv3-chrP.Zea_mays.AGPv3-chrM+chrP.bowtie.k3m2.wig
z       = 5
max_gap = 0u
fill_under = yes
fill_color = black
color   = black
min     = 0
max     = 36
r0      = 0.88r
r1      = 0.93r
</plot>

<plot>
type = tile
file = Zea_mays.AGPv3.19.fixed.chloroplast.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 = 0.86r
r1 = 0.88r
</plot>

<plot>
type = tile
file = Zea_mays.AGPv3.19.fixed.chloroplast.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 = 0.84r
r1 = 0.86r
</plot>

<plot>
type = tile
file = Zea_mays.AGPv3.19.fixed.chloroplast.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 = 0.80r
r1 = 0.84r
</plot>

<plot>
type = tile
file = Zea_mays.AGPv3.19.fixed.chloroplast.gff3.pseudogene.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 = 0.78r
r1 = 0.80r
</plot>

<plot>
type = tile
file = Zea_mays.AGPv3.19.fixed.chloroplast.gff3.pseudogene.plus.tiles
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = lblue
color = lblue
r0 = 0.76r
r1 = 0.78r
</plot>


<plot>
show    = yes
file    = 31-organelles-nucleus-merged-k3m2-Zea_mays/tassel1-ChIP-GSM957186.36mers.chloroplast.plus.RPM.wig
z       = 5
max_gap = 0u
fill_under = yes
fill_color = red
color   = red
min     = 0
max     = 112
r0      = 0.64r
r1      = 0.74r
</plot>


<plot>
show    = yes
file    = 31-organelles-nucleus-merged-k3m2-Zea_mays/tassel1-Total_input-GSM957187.36mers.chloroplast.plus.RPM.wig
z       = 5
max_gap = 0u
fill_under = yes
fill_color = blue
color   = blue
min     = 0
max     = 112
r0      = 0.44r
r1      = 0.54r
</plot>


<plot>
show    = yes
file    = 31-organelles-nucleus-merged-k3m2-Zea_mays/tassel1-ChIP-GSM957186.36mers.chloroplast.minus.RPM.wig.sign_flipped
z       = 5
max_gap = 0u
orientation = in
fill_under = yes
fill_color = black
color   = orange
min     = 0
max     = 112
r0      = 0.54r
r1      = 0.64r
</plot>


<plot>
show    = yes
file    = 31-organelles-nucleus-merged-k3m2-Zea_mays/tassel1-Total_input-GSM957187.36mers.chloroplast.minus.RPM.wig.sign_flipped
z       = 5
max_gap = 0u
orientation = in
fill_under = yes
fill_color = black
color   = yellow
min     = 0
max     = 112
r0      = 0.34r
r1      = 0.44r
</plot>

</plots>
