plots.conf

<plots>

<plot>
type        = tile
file        = ./Mitochondrial_elements.txt
r1          = 0.95r
r0          = 0.71r
orientation = center

layers      = 11
margin      = 0.02u
thickness   = 25p
padding     = 4

layers_overflow       = collapse
layers_overflow_color = red

stroke_thickness = 1
stroke_color     = black
color            = green

<backgrounds>
<background>
color = vvlgrey
</background>
</backgrounds>

<rules>
<rule>
condition  = var(value) =~ /trn/
color      = red
</rule>

<rule>
condition  = var(value) =~ /rrn/
color      = blue
</rule>

<rule>
condition  = var(value) =~ /AT-rich/
color      = grey
</rule>

<rule>
condition  = var(value) =~ /TRU/
color      = grey
</rule>

<rule>
condition  = var(value) =~ /IGNOREME/
color      = grey
</rule>

<rule>
condition  = var(value) =~ /OH/
color      = grey
</rule>

<rule>
condition  = var(value) =~ /CR/
color      = grey
</rule>

<rule>
color      = green  
flow = stop
</rule>

</rules>

</plot>

################### non tRNAs
<plot>
type = text
orientation = inside
color      = black
label_font = default
label_size = 46p
file = ./no_tRNA_Mitochondrial_elements.txt
r1   = 1.2r
r0   = 0.90r
show_links     = no

label_parallel = yes
label_snuggle = yes
# shift label up to its height in pixels in the angular direction
max_snuggle_distance      = 1.5r
snuggle_sampling          = 4
snuggle_tolerance         = 0.25r
snuggle_link_overlap_test = yes 
snuggle_link_overlap_tolerance = 2p
snuggle_refine            = yes
</plot>

################### tRNAs
<plot>
type = text
orientation = in
color      = black
label_font = default
label_size = 24p
file = ./yes_tRNA_Mitochondrial_elements.txt
r1   = 0.85r
r0   = 0.70r
show_links     = no

label_parallel = no
label_snuggle = yes
# shift label up to its height in pixels in the angular direction
max_snuggle_distance      = 2r
snuggle_sampling          = 2
snuggle_tolerance         = 0.25r
snuggle_link_overlap_test = yes
snuggle_link_overlap_tolerance = 2p
snuggle_refine            = yes
</plot>

</plots>