<<include colors_fonts_patterns.conf>>

<<include etc/housekeeping.conf>>

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

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

karyotype   = chrM.karyotype

chromosomes_units           = 10
chromosomes_display_default = no
chromosomes                 = chrM

<plots>

type      = histogram
thickness = 2

<plot>
show    = yes
file    = mappability/TAIR10.36mers.TAIR10.bowtie.mappability.unique.chrM.wig
z       = 5
max_gap = 0u
fill_under = yes
fill_color = dred
color   = dred
min     = 0
max     = 36
r0      = 0.88r
r1      = 0.98r
</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 = 0.86r
r1 = 0.88r
</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 = 0.84r
r1 = 0.86r
</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 = 0.80r
r1 = 0.84r
</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 = 0.78r
r1 = 0.80r
</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 = purple
color = purple
r0 = 0.76r
r1 = 0.78r
</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 = 0.74r
r1 = 0.76r
</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    = 19-organelles-nucleus-merged/LEAFY-ctrl-rep1-GSM605654.36mers.chrM.plus.RPM.wig
z       = 5
max_gap = 0u
fill_under = yes
fill_color = black
color   = yellow
min     = 0
max     = 25
r0      = 0.59r
r1      = 0.64r
</plot>


<plot>
show    = yes
file    = 19-organelles-nucleus-merged/LEAFY-samp-rep1-GSM605656.36mers.chrM.plus.RPM.wig
z       = 5
max_gap = 0u
fill_under = yes
fill_color = black
color   = yellow
min     = 0
max     = 19
r0      = 0.69r
r1      = 0.74r
</plot>


<plot>
show    = yes
file    = 19-organelles-nucleus-merged/LEAFY-ctrl-rep1-GSM605654.36mers.chrM.minus.RPM.wig.sign_flipped
z       = 5
max_gap = 0u
orientation = in
fill_under = yes
fill_color = yellow
color   = black
min     = 0
max     = 29
r0      = 0.54r
r1      = 0.59r
</plot>


<plot>
show    = yes
file    = 19-organelles-nucleus-merged/LEAFY-samp-rep1-GSM605656.36mers.chrM.minus.RPM.wig.sign_flipped
z       = 5
max_gap = 0u
orientation = in
fill_under = yes
fill_color = yellow
color   = black
min     = 0
max     = 24
r0      = 0.64r
r1      = 0.69r
</plot>

</plots>
