<<include colors_fonts_patterns.conf>>

# <colors>
# colors.conf will import Brewer palettes, HSV colors and color lists
# <<include etc/colors.conf>>
# </colors>

<<include hg19.housekeeping.conf>>

<<include hg19.ideogram.conf>>
<<include hg19.ticks.conf>>

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

karyotype   = hg19.chrM.karyotype

chromosomes_units           = 10
chromosomes_display_default = no
chromosomes                 = chrM

<plots>

<plot>
type      = histogram
thickness = 2
show    = yes
file    = HepG2-TFAM-SAB1401382-Rep5-SL35477.chrM.v0.plus.wig
z       = 5
max_gap = 0u
fill_under = yes
fill_color = dred
color   = dred
min     = 0
max     = 3400
r0      = 0.88r
r1      = 0.98r
</plot>

<plot>
type      = histogram
thickness = 2
show    = yes
file    = HepG2-TFAM-SAB1401382-Rep5-SL35477.chrM.v0.minus.wig
z       = 5
max_gap = 0u
orientation = in
fill_under = yes
fill_color = blue
color   = blue
min     = 0
max     = 3400
r0      = 0.78r
r1      = 0.88r
</plot>

<plot>
type = tile
file = hg19.chrM.minus.protein_coding.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = dorange
color = dorange
r0 = 0.65r
r1 = 0.66r
</plot>

<plot>
type = tile
file = hg19.chrM.plus.protein_coding.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = green
color = green
r0 = 0.63r
r1 = 0.65r
</plot>

<plot>
type = tile
file = hg19.chrM.plus.rRNA.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = blue
color = blue
r0 = 0.62r
r1 = 0.63r
</plot>

<plot>
type = tile
file = hg19.chrM.plus.tRNA.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = purple
color = purple
r0 = 0.60r
r1 = 0.62r
</plot>

<plot>
type = tile
file = hg19.chrM.minus.tRNA.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = gpos75
color = gpos75
r0 = 0.58r
r1 = 0.60r
</plot>

<plot>
type = text
file = hg19.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>
type = text
file = hg19.chrM.tRNA.text
color      = black
label_font = bold
label_size = 22p
padding = 2p
rpadding = 2p
z       = 2
r0 = 1.03r
r1 = 1.08r
</plot>

# <plot>
# type      = histogram
# thickness = 2
# show    = yes
# file    = chrM.GC10bp.wig
# z       = 5
# max_gap = 0u
# fill_under = yes
# fill_color = dred
# color   = dred
# min     = 0.2
# max     = 0.8
# r0      = 1.15r
# r1      = 1.20r
# </plot>

<plot>
type = tile
file = hg19.chrM.LSP.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = red
color = red
r0 = 0.965r
r1 = 0.975r
</plot>

<plot>
type = tile
file = hg19.chrM.HSP.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = blue
color = blue
r0 = 0.965r
r1 = 0.975r
</plot>

<plot>
type = tile
file = hg19.chrM.LSP-TFAM.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = dred
color = dred
r0 = 0.985r
r1 = 0.995r
</plot>

<plot>
type = tile
file = hg19.chrM.HSP.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = dblue
color = dblue
r0 = 0.985r
r1 = 0.995r
</plot>

<plot>
type = tile
file = hg19.chrM.D-loop.tile
layers = 2
layers_overflow = hide
margin = 0.2u
thickness = 12
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = black
color = black
r0 = 0.945r
r1 = 0.955r
</plot>

</plots>
