<<include colors_fonts_patterns.conf>>

<<include etc/housekeeping.conf>>

<<include sacCer3.chrM.ideogram.conf>>
<<include sacCer3.chrM.ticks.conf>>

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

karyotype   = sacCer3.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/sacCer3/mappability/sacCer3.36mers.sacCer3.bowtie.v2.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 = Saccharomyces_cerevisiae.SacCer_Apr2011.20.chrM.protein_coding.genes.plus.tile
layers = 6
layers_overflow = hide
margin = 0.2u
thickness = 28
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = black
color = yellow
r0 = 0.72r
r1 = 0.88r
</plot>

<plot>
type = tile
file = Saccharomyces_cerevisiae.SacCer_Apr2011.20.chrM.rRNA.genes.plus.tile
layers = 6
layers_overflow = hide
margin = 0.2u
thickness = 36
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = black
color = blue
r0 = 0.80r
r1 = 0.88r
</plot>

<plot>
type = tile
file = Saccharomyces_cerevisiae.SacCer_Apr2011.20.chrM.tRNA.genes.plus.tile
layers = 6
layers_overflow = hide
margin = 0.2u
thickness = 36
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = grey
color = grey
r0 = 0.80r
r1 = 0.88r
</plot>

<plot>
type = tile
file = Saccharomyces_cerevisiae.SacCer_Apr2011.20.chrM.tRNA.genes.minus.tile
layers = 6
layers_overflow = hide
margin = 0.2u
thickness = 36
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = red
color = red
r0 = 0.80r
r1 = 0.88r
</plot>

<plot>
type = tile
file = Saccharomyces_cerevisiae.SacCer_Apr2011.20.chrM.ncRNA.genes.plus.tile
layers = 6
layers_overflow = hide
margin = 0.2u
thickness = 36
padding = 6
orientation = out
stroke_thickness = 1
stroke_color = orange
color = orange
r0 = 0.80r
r1 = 0.88r
</plot>

<plot>
type = text
file = Saccharomyces_cerevisiae.SacCer_Apr2011.20.chrM.protein_coding.genes.plus.text
color      = black
label_font = bold
label_size = 28p
label_parallel   = no
padding = 15p
rpadding = 15p
z       = 1
r0 = 1.02r
r1 = 1.22r
</plot>

<plot>
type = text
file = Saccharomyces_cerevisiae.SacCer_Apr2011.20.chrM.tRNA.genes.text
color      = black
label_font = bold
label_size = 8p
label_parallel  = no
padding = 2p
rpadding = 2p
z       = 2
r0 = 1.03r
r1 = 1.08r
</plot>


<plot>
show    = yes
file    = 9-Saccharomyces_cerevisiae/SEG14ChIP_rep2-GSM511913.sacCer3.25mers.unique.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     = 13
r0      = 0.62r
r1      = 0.67r
</plot>


<plot>
show    = yes
file    = 9-Saccharomyces_cerevisiae/SEG14ChIP_rep2-GSM511913.sacCer3.25mers.unique.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     = 13
r0      = 0.67r
r1      = 0.72r
</plot>


<plot>
show    = yes
file    = 9-Saccharomyces_cerevisiae/SEG14input-GSM512020.sacCer3.25mers.unique.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     = 143
r0      = 0.52r
r1      = 0.57r
</plot>


<plot>
show    = yes
file    = 9-Saccharomyces_cerevisiae/SEG14input-GSM512020.sacCer3.25mers.unique.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     = 231
r0      = 0.57r
r1      = 0.62r
</plot>

</plots>
