
show_links      = yes
show_heatmaps   = yes
show_highlights = yes
show_scatter    = yes
show_histogram  = yes
show_text       = yes

<<include karyotype.and.layout.conf>>

### links

<links>
show          = __$CONF{show_links}__
ribbon        = yes
flat          = yes
radius        = 0.45r-55p
bezier_radius = 0r
color         = black_a5

<link ratbundle>
file = exampledata/rn.bundle.txt
<<include link.rules.conf>>
</link>

<link mousebundle>
file = exampledata/mm.bundle.txt
<<include link.rules.conf>>
</link>

</links>

### plots

<plots>

<<include highlights.conf>>

# some large human genes (list contains genes > 250kb in size)

<plot>
show   = __$CONF{show_text}__
type   = text
file   = exampledata/genes.txt
color  = black
r0     = 0.415r
r1     = 0.73r
label_size = 12p
label_font = default

rpadding = 0r
padding  = 0.1r

label_snuggle        = yes
max_snuggle_distance = 1r
snuggle_sampling     = 1
snuggle_tolerance    = 0.25r

show_links     = yes
link_dims      = 4p,2p,5p,2p,2p
link_thickness = 2p
link_color     = grey

<rules>
<rule>
importance = 100
condition  = _LABEL_ =~ /omim/
color      = blue # green
flow       = continue
</rule>
<rule>
importance = 100
condition  = _LABEL_ =~ /cancer/
color      = red
label_font = bold
flow       = continue
</rule>
<rule>
importance = 90
condition  = 1
value      = eval( my $x=_LABEL_; $x=~ s/_.+//; $x )
</rule>
</rules>

</plot>

# human->mouse and human->rat chain heatmaps

<plot>
show   = __$CONF{show_heatmaps}__
type   = heatmap
file   = exampledata/heatmap.hs.mm.20e6.txt
color  = blues-9-seq
min    = 0
max    = .20e6
r0     = 0.765r
r1     = 0.785r
stroke_color     = white
stroke_thickness = 1p
</plot>

<plot>
show   = __$CONF{show_heatmaps}__
type   = heatmap
file   = exampledata/heatmap.hs.rn.20e6.txt
color  = reds-9-seq
min    = 0
max    = .20e6
r0     = 0.79r
r1     = 0.81r
stroke_color     = white
stroke_thickness = 1p
</plot>

<plot>
show   = __$CONF{show_heatmaps}__
type   = heatmap
file   = exampledata/heatmap.hs.mm.10e6.txt
color  = blues-9-seq
min    = 0
max    = .10e6
r0     = 0.895r
r1     = 0.915r
stroke_color     = white
stroke_thickness = 1p
</plot>

<plot>
show   = __$CONF{show_heatmaps}__
type   = heatmap
file   = exampledata/heatmap.hs.rn.10e6.txt
color  = reds-9-seq
min    = 0
max    = .10e6
r0     = 0.92r
r1     = 0.94r
stroke_color     = white
stroke_thickness = 1p
</plot>

<<include mmchain.heatmap.allchrs.conf>>
<<include rnchain.heatmap.allchrs.conf>>

<<include rnchain.scatter.allchrs.conf>>
<<include mmchain.scatter.allchrs.conf>>

################################################################
# histograms on human chromosomes

# total mouse chain, with scatter plot
# oriented outward
<plot>
show   = __$CONF{show_histogram}__
type = histogram
file = exampledata/heatmap.hs.mm.20e6.txt
min  = 0
max  = .5e6
fill_under = yes
fill_color = blues-5-seq-4_a5
r0 = 1r
r1 = 1r+180p
orientation = out
</plot>

<plot>
show   = __$CONF{show_histogram}__
type = scatter
file = exampledata/heatmap.hs.mm.5e6.txt
min  = 0
max  = .5e6
glyph = circle
glyph_size = 10
fill_color = blues-5-seq-5
r0 = 1r
r1 = 1r+180p
</plot>

# total rat chain, with scatter plot
# oriented inward
<plot>
show   = __$CONF{show_histogram}__
type = histogram
file = exampledata/heatmap.hs.rn.20e6.txt
min  = 0
max  = .5e6
fill_under = yes
fill_color = reds-5-seq-4_a5
r0 = 1r
r1 = 1r+180p
orientation = in
</plot>

<plot>
show   = __$CONF{show_histogram}__
type = scatter
file = exampledata/heatmap.hs.rn.5e6.txt
min  = 0
max  = .5e6
glyph = circle
glyph_size = 10
fill_color = reds-5-seq-5
r0 = 1r
r1 = 1r+180p
orientation = in
</plot>

</plots>

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

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

<colors>
<<include etc/colors.conf>>
<<include etc/brewer.conf>>
</colors>

<fonts>
<<include etc/fonts.conf>>
</fonts>

<<include etc/housekeeping.conf>>

