changeset 8:198b83bf871e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/circos.conf	Wed Nov 30 13:38:28 2016 -0500
@@ -0,0 +1,352 @@
+
+# You can control which tracks to show. 
+# 
+# These can be set at the command line using
+#
+# circos -param show_labels=no -param show_sv_total=no ...
+#
+# You can verify settings using -cdump 
+#
+# circos -cdump | grep show_
+
+show_sv  = yes
+show_cnv = 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
+
+################################################################
+# Colors are referenced using their name e.g. "amp" in 
+# parameters directly
+#
+# fill_color = amp
+
+<colors>
+amp   = vdred
+gain  = red
+neut  = dgrey 
+hetd  = blue
+homd  = vdblue
+
+cnv-1 = amp
+cnv-2 = gain
+cnv-3 = hetd
+cnv-4 = homd
+
+sv-1  = grey
+sv-2  = vdblue
+sv-3  = vdred
+sv-4  = blue
+sv-5  = red
+sv-6  = lorange
+sv-7  = vdorange
+sv-8  = vlgrey
+
+# color lists, sorted numerically in increasing order
+# using the text matched in capture brackets
+sv    = sv-(\d+)
+cnv   = cnv-(\d+)
+</colors>
+
+chromosomes_units           = 1
+chromosomes_display_default = yes
+chromosomes                 = -hsY
+
+#chromosomes_display_default = no
+#chromosomes                 = /hs[1234]$/
+
+karyotype = data/karyotype.txt
+
+################################################################
+# For auto-spacing and positioning of tracks
+
+# Start, width and spacing of tracks
+track_r0 = 0.99
+track_w  = 0.1
+track_s  = 0.025
+
+# width and spacing of individual SV type tracks
+sv_w     = 0.0   # 
+sv_s     = 0.015 # 
+
+# Order in which SV and CNV tracks are shown
+sv_types = nonsense_mutation,frame_shift_del,frame_shift_ins,in_frame_del,in_frame_ins,splice_site,nonstop_mutation,missense_mutation
+cnv_types = amp,gain,hetd,homd
+
+<plots>
+
+# All plot blocks share data from the same file
+file             = data/mutations.txt
+stroke_thickness = 0
+
+################################################################
+# Gene labels, filtered by SNV total
+<plot>
+show       = conf(show_labels)
+type       = text
+r1         = dims(ideogram,radius_outer) + 500p
+r0         = dims(ideogram,radius_outer) + 20p + conf(track_w)r
+
+label_size           = 14
+label_snuggle        = yes
+max_snuggle_distance = 3r
+snuggle_sampling     = 1
+snuggle_tolerance    = 0.25r
+
+show_links    = yes
+link_color    = black
+link_dims     = 0p,5p,5p,5p,0p
+
+<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>
+
+################################################################
+# SV total 
+
+<plot>
+show       = conf(show_sv_total)
+type       = histogram
+r1         = dims(ideogram,radius_outer) + 20p + conf(track_w)r
+r0         = dims(ideogram,radius_outer) + 20p
+min        = 0
+#max        = 20
+fill_color = black
+
+<<include white.bin.conf>>
+
+<axes>
+<axis>
+spacing = 0.1r
+</axis>
+</axes>
+
+<rules>
+<rule>
+condition = 1
+value     = eval(var(sv_tot))
+flow      = continue
+</rule>
+</rules>
+</plot>
+
+################################################################
+# SV protein position recurrence
+
+<plot>
+show      = conf(show_svaa)
+type      = heatmap
+r1        = dims(ideogram,radius_outer)+15p
+r0        = dims(ideogram,radius_outer)+5p
+min       = 2
+max       = 5
+color     = grey,orange,red,dred
+<rules>
+<rule>
+condition = 1
+value     = eval(var(svaa_max_n))
+flow      = continue
+</rule>
+<rule>
+condition = var(value) == 1
+show      = no
+</rule>
+</rules>
+</plot>
+
+
+################################################################
+# SV stacked barplot 
+
+<plot>
+show = conf(show_sv_stack)
+file = data/mutations.stacked.sv.txt
+orientation = in
+type = histogram
+r1   = eval(sprintf("%fr",conf(track_r0)))
+r0   = eval(sprintf("%fr",conf(track_r0)-conf(track_w)))
+min  = 0
+max  = 1
+fill_color           = sv
+normalize_bin_values = yes
+<<include white.bin.conf>>
+<<include track.counter.conf>>
+</plot>
+
+<<include sv.type.conf>>
+<<include sv.type.conf>>
+<<include sv.type.conf>>
+<<include sv.type.conf>>
+<<include sv.type.conf>>
+<<include sv.type.conf>>
+<<include sv.type.conf>>
+
+###############################################################
+# +/- CNV histograms
+
+<plot>
+show = conf(show_cnv_plus_minus)
+type = histogram
+<<include r0r1.conf>>
+max = 20
+min = -20
+fill_color = gain
+<<include white.bin.conf>>
+<axes>
+<axis>
+spacing = .1r
+</axis>
+<axis>
+position  = 0
+thickness = 2
+</axis>
+</axes>
+<backgrounds>
+<background>
+color = vvlgrey
+</background>
+</backgrounds>
+<rules>
+<rule>
+condition  = 1
+value      = eval(var(cnv_plus))
+</rule>
+</rules>
+</plot>
+
+<plot>
+show = conf(show_cnv_plus_minus)
+type = histogram
+<<include r0r1.conf>>
+max  = 20
+min  = -20
+fill_color = homd
+<<include white.bin.conf>>
+<<include track.counter.conf>>
+<rules>
+<rule>
+condition  = 1
+value      = eval(-var(cnv_minus))
+</rule>
+</rules>
+</plot>
+
+################################################################
+# CNV stacked bar plot
+
+<plot>
+show = conf(show_cnv_stack)
+file = data/mutations.stacked.cnv.txt
+orientation = in
+type = histogram
+<<include r0r1.conf>>
+min  = 0
+max  = 1
+fill_color = cnv
+normalize_bin_values = yes
+<<include white.bin.conf>>
+<<include track.counter.conf>>
+</plot>
+
+<plot>
+show = conf(show_cnv_copy_number)
+type = histogram
+<<include r0r1.conf>>
+min  = 0
+max  = 4
+<<include white.bin.conf>>
+<<include track.counter.conf>>
+<axes>
+<axis>
+position = 2
+color    = black
+</axis>
+<axis>
+spacing  = 0.5
+y1       = 1
+color    = homd
+</axis>
+<axis>
+spacing  = 0.5
+y0       = 3
+color    = amp
+</axis>
+</axes>
+<rules>
+<rule>
+condition = !var(cnv_top_n)
+show      = no
+</rule>
+<rule>
+condition  = 1
+value      = eval(var(cnv_top_avg))
+fill_color = eval(lc var(cnv_top_type))
+</rule>
+</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>
+<<include etc/image.conf>>
+</image>
+<<include etc/housekeeping.conf>>
+<<include etc/colors_fonts_patterns.conf>>
+<<include ideogram.conf>>
+#<<include ticks.conf>>
+max_points_per_track* = 50000