<<include colors_fonts_patterns.conf>>

<<include etc/housekeeping.conf>>

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

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

<spacing>
default = 0.01r
</spacing>

karyotype = dm3.karyotype

chromosomes_units           = 10000000
chromosomes_display_default = no
chromosomes                 = chr2L;chr2R;chr3L;chr3R;chr4;chrM;chrUextra;chrU;chrX;chrYHet

# <plot>
# type = text
# file = 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 = tile
# file = 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>

type      = histogram
thickness = 2

<plot>
show    = yes
file    = dm3.1000bp.readCounts.int.shPiwi-vs-shWhite.res.pval0.05.txt-down.merged.bed
z       = 5
max_gap = 0u
fill_under = yes
fill_color = red
color   = red
min     = 0
max     = 1
r0      = 0.80r
r1      = 0.95r
</plot>

<plot>
show    = yes
file    = ../repeatMask.txt.LTR+LINE+DNA.bed
z       = 5
max_gap = 0u
fill_under = yes
fill_color = orange
color   = orange
min     = 0
max     = 1
r0      = 0.65r
r1      = 0.80r
</plot>


</plots>