changeset 10:417f984cd2e2 draft default tip

Uploaded

--- a/etc/circos.conf	Wed Nov 30 13:40:45 2016 -0500
+++ b/etc/circos.conf	Wed Nov 30 13:41:12 2016 -0500
@@ -9,16 +9,20 @@
 #
 # circos -cdump | grep show_
 
-show_labels   = yes
-show_sv_total = yes
-show_svaa     = yes
-show_sv_stack = yes
-show_sv_types = yes
+show_sv  = yes
+show_cnv = yes
 
-show_cnv_stack = yes
-show_cnv_types = yes
-show_cnv_plus_minus = yes
+show_labels          = yes
+show_sv_total        = conf(show_sv) # yes
+show_svaa            = conf(show_sv) # yes
+show_sv_stack        = conf(show_sv) # yes
+show_sv_types        = conf(show_sv) # yes
+
+show_cnv_stack       = yes # yes
+show_cnv_types       = yes # yes
+show_cnv_plus_minus  = yes # yes
 show_cnv_copy_number = yes
+show_cnv_tiles       = yes
 
 sv_label_min  = 5
 
@@ -32,8 +36,8 @@
 amp   = vdred
 gain  = red
 neut  = dgrey 
-homd  = blue
-hetd  = vdblue
+hetd  = blue
+homd  = vdblue
 
 cnv-1 = amp
 cnv-2 = gain
@@ -106,13 +110,26 @@
 
 <rules>
 <rule>
+importance = 1
 condition  = var(sv_tot) < conf(sv_label_min)
 show       = no
 </rule>
 <rule>
+importance = 3
+condition  = var(label_gene) > 0
+show       = yes
+label_font = bold
+color = blue
+</rule>
+
+
+
+<rule>
+importance = 2
 condition  = var(sv_tot) > 2*conf(sv_label_min)
 label_font = bold
 </rule>
+
 </rules>
 </plot>
 
@@ -267,24 +284,24 @@
 show = conf(show_cnv_copy_number)
 type = histogram
 <<include r0r1.conf>>
-min  = -2
-max  = 2
+min  = 0
+max  = 4
 <<include white.bin.conf>>
 <<include track.counter.conf>>
 <axes>
 <axis>
-position = 0
+position = 2
 color    = black
 </axis>
 <axis>
 spacing  = 0.5
-y1       = 0
-color    = lred
+y1       = 1
+color    = homd
 </axis>
 <axis>
 spacing  = 0.5
-y0       = 0
-color    = lblue
+y0       = 3
+color    = amp
 </axis>
 </axes>
 <rules>
@@ -300,6 +317,29 @@
 </rules>
 </plot>
 
+<plot>
+show        = conf(show_cnv_tiles)
+file        = data/cnv.tiles.txt
+type        = tile
+orientation = in
+color       = black
+layers      = 10
+thickness   = 10
+padding     = 3
+margin      = 0u
+sort           = size
+sort_direction = desc
+<<include r0r1.conf>>
+r0* = 0r
+<<include track.counter.conf>>
+<rules>
+<rule>
+condition = 1
+color     = eval(var(value))
+</rule>
+</rules>
+</plot>
+
 </plots>
 
 <image>