changeset 9:98b02b71d052 draft

Deleted selected files

--- a/circos.conf	Wed Nov 30 13:38:28 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,352 +0,0 @@
-
-# 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