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changeset 1:916c60c717a6 draft

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planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/oncocircos commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
author morinlab
date Tue, 11 Oct 2016 14:23:01 -0400
parents b77ab858eac1
children 55571b9980b0
files etc/circos.conf~ etc/cnv.type.conf~ etc/color.conf~ etc/ideogram.conf~ etc/ideogram.position.conf~ etc/library.conf~ etc/r0r1.conf~ etc/rule.type.conf~ etc/sv.type.conf~ etc/ticks.conf~ etc/track.counter.conf~ etc/white.bin.conf~
diffstat 12 files changed, 0 insertions(+), 498 deletions(-) [+]
line wrap: on
line diff
--- a/etc/circos.conf~	Mon Sep 12 16:23:26 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,309 +0,0 @@
-
-show_labels   = yes
-show_sv_total = yes
-show_svaa     = yes
-show_sv_stack = yes
-show_sv_types = yes
-
-show_cnv_stack = yes
-show_cnv_types = yes
-show_cnv_plus_minus = yes
-show_cnv_copy_number = yes
-
-sv_label_min  = 5
-
-show_cnv = no # old
-
-<colors>
-amp   = dred
-gain  = red
-neut  = dgrey  # not used
-homd  = blue
-hetd  = dblue
-
-cnv-1 = amp
-cnv-2 = gain
-cnv-3 = hetd
-cnv-4 = homd
-
-sv-1  = black
-sv-2  = dblue
-sv-3  = dred
-sv-4  = blue
-sv-5  = red
-sv-6  = lorange
-sv-7  = orange
-sv-8  = vlgrey
-
-sv    = sv-(\d+)
-cnv   = cnv-(\d+)
-</colors>
-
-chromosomes_units           = 1
-chromosomes_display_default = yes
-chromosomes                 = -hsY # hs1;hs2;hs3
-
-karyotype = data/karyotype.txt
-
-# SV by type
-sv_r0    = 0.90  # outer track radius
-sv_w     = 0.0   # track width
-sv_s     = 0.015 # track width for smaller tracks
-# this is the order of the SV type tracks, from outside in
-sv_types = nonsense_mutation,frame_shift_del,frame_shift_ins,in_frame_del,in_frame_ins,splice_site,nonstop_mutation,missense_mutation
-
-# CNV by type
-cnv_r0    = 0.70  # outer track radius
-cnv_w     = 0.0   # track width
-cnv_s     = 0.015 # track width for smaller tracks
-cnv_types = amp,gain,hetd,homd
-
-<plots>
-
-file             = data/mutations.txt
-stroke_thickness = 0
-
-################################################################
-# SV total 
-
-<plot>
-show       = conf(show_sv_total)
-type       = histogram
-r1         = dims(ideogram,radius_outer) + 100p
-r0         = dims(ideogram,radius_outer) + 20p
-min        = 0
-max        = 20
-fill_color = black
-
-<axes>
-<axis>
-spacing   = 4
-</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>
-
-################################################################
-# Gene labels, filtered by SNV total
-<plot>
-show       = conf(show_labels)
-type       = text
-r1         = dims(ideogram,radius_outer) + 500p
-r0         = dims(ideogram,radius_outer) + 100p
-
-label_snuggle = yes
-show_links    = yes
-
-label_size    = 14
-link_color    = black
-link_dims     = 0p,5p,5p,5p,0p
-
-<rules>
-<rule>
-condition  = var(sv_tot) < conf(sv_label_min)
-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   = 0.995r
-r0   = 0.925r
-min  = 0
-max  = 1
-fill_color           = sv
-normalize_bin_values = yes
-</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 stacked bar plot
-
-<plot>
-show = conf(show_cnv_stack)
-file = data/mutations.stacked.cnv.txt
-orientation = in
-type = histogram
-r1   = 0.775r
-r0   = 0.725r
-min  = 0
-max  = 1
-fill_color = cnv
-normalize_bin_values = yes
-</plot>
-
-################################################################
-# CNV in samples, by event type
-
-<<include cnv.type.conf>>
-<<include cnv.type.conf>>
-<<include cnv.type.conf>>
-<<include cnv.type.conf>>
-
-###############################################################
-# +/- CNV histograms
-
-<plot>
-show = conf(show_cnv_plus_minus)
-type = histogram
-r1   = 0.625r
-r0   = 0.55r
-max  = 20
-min  = -20
-fill_color = blue
-<axes>
-<axis>
-spacing = 5
-</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
-r1   = 0.625r
-r0   = 0.55r
-max  = 20
-min  = -20
-fill_color = red
-<rules>
-<rule>
-condition  = 1
-value      = eval(-var(cnv_minus))
-</rule>
-</rules>
-</plot>
-
-<plot>
-show = conf(show_cnv)
-type = histogram
-r1   = 0.775r
-r0   = 0.725r
-min  = 0
-
-<axes>
-<axis>
-spacing = 10
-</axis>
-</axes>
-
-<rules>
-<rule>
-condition  = !var(cnv_tot)
-show       = no
-</rule>
-<rule>
-condition  = 1
-value      = eval(var(cnv_tot))
-fill_color = eval(lc var(cnv_type))
-</rule>
-</rules>
-
-</plot>
-
-<plot>
-show = conf(show_cnv_copy_number)
-type = histogram
-r1   = 0.525r
-r0   = 0.40r
-min  = -2
-max  = 2
-<axes>
-<axis>
-position = 0
-color    = black
-</axis>
-<axis>
-spacing  = 0.5
-y1       = 0
-color    = lred
-</axis>
-<axis>
-spacing  = 0.5
-y0       = 0
-color    = lblue
-</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>
-
-</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
--- a/etc/cnv.type.conf~	Mon Sep 12 16:23:26 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-<plot>
-show = conf(show_sv_types)
-init_counter           = sv:0
-post_increment_counter = sv:1
-type = scatter
-r1   = eval(sprintf("%fr",conf(sv_r0) - counter(sv)*(conf(sv_w)+conf(sv_s))))
-r0   = eval(sprintf("%fr",conf(sv_r0) - counter(sv)*(conf(sv_w)+conf(sv_s)) - conf(sv_w)))
-min  = 0
-max  = 0
-color = eval(sprintf("dark2-8-qual-%d",1+counter(sv)))
-<axes>
-<axis>
-position = 0
-</axis>
-</axes>
-<rules>
-<rule>
-condition  = 1
-type       = eval(sprintf("sv_%s",(split(",",qq{conf(sv_types)}))[counter(sv)]))
-flow       = continue
-</rule>
-<rule>
-condition  = !var(var(type))
-show       = no
-</rule>
-<rule>
-condition  = 1
-value      = 0
-glyph_size = eval(remap_int(var(var(type)),1,10,10,30))
-</rule>
-</rules>
-</plot>
--- a/etc/color.conf~	Mon Sep 12 16:23:26 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-color = eval((counter(plot)%3) == 0 ? "blue" : (counter(plot)%3) == 1 ? "orange,red,dred" : "red")
--- a/etc/ideogram.conf~	Mon Sep 12 16:23:26 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-
-<ideogram>
-
-<spacing>
-
-default = 0.002r
-break   = 0.25r
-
-axis_break         = yes
-axis_break_style   = 2
-axis_break_at_edge = yes
-
-<<include breaks.conf>>
-
-</spacing>
-
-<<include ideogram.position.conf>>
-<<include ideogram.label.conf>>
-
-</ideogram>
-
--- a/etc/ideogram.position.conf~	Mon Sep 12 16:23:26 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-radius           = 0.85r
-thickness        = 10p
-fill             = yes
-fill_color       = black
-stroke_thickness = 1
-stroke_color     = black
--- a/etc/library.conf~	Mon Sep 12 16:23:26 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-<plot>
-file = data/lib.eval(counter(library)).txt
-<<include color.conf>>
-<<include r0r1.conf>>
-<rules>
-<<include rule.type.conf>>
-</rules>
-</plot>
-
-<plot>
-file = data/lib.eval(counter(library)).txt
-<<include color.conf>>
-<<include r0r1.conf>>
-<rules>
-<<include rule.type.conf>>
-</rules>
-</plot>
-
-<plot>
-file = data/lib.eval(counter(library)).txt
-<<include color.conf>>
-<<include r0r1.conf>>
-<rules>
-<<include rule.type.conf>>
-</rules>
-
-post_increment_counter = library:1
-
-</plot>
--- a/etc/r0r1.conf~	Mon Sep 12 16:23:26 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-r1 = eval(sprintf("%fr",((counter(plot)%3==2)?-conf(tw):0)      + ((counter(plot)%3==0)?conf(tws):0)          + conf(t0) - counter(library)*(conf(tw)+conf(ts))))
-r0 = eval(sprintf("%fr",((counter(plot)%3==2)?-conf(tws):0) + ((counter(plot)%3==0)?+conf(tw):0) + conf(t0) - counter(library)*(conf(tw)+conf(ts)) - conf(tw)))
--- a/etc/rule.type.conf~	Mon Sep 12 16:23:26 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-<rule>
-condition = var(class) ne "all"
-show      = no
-</rule>
-<rule>
-condition = (counter(plot)%3) == 0 && var(type) eq "ins"
-show      = yes
-</rule>
-<rule>
-condition = (counter(plot)%3) == 1 && var(type) eq "snp"
-show      = yes
-</rule>
-<rule>
-condition = (counter(plot)%3) == 2 && var(type) eq "del"
-show      = yes
-</rule>
-<rule>
-condition = 1
-show      = no
-</rule>
-
--- a/etc/sv.type.conf~	Mon Sep 12 16:23:26 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-<plot>
-show = conf(show_sv_types)
-init_counter           = sv:0
-post_increment_counter = sv:1
-type = scatter
-r1   = eval(sprintf("%fr",conf(sv_r0) - counter(sv)*(conf(sv_w)+conf(sv_s))))
-r0   = eval(sprintf("%fr",conf(sv_r0) - counter(sv)*(conf(sv_w)+conf(sv_s)) - conf(sv_w)))
-min  = 0
-max  = 0
-color = eval(sprintf("sv-%d",1+counter(sv)))
-<axes>
-<axis>
-position = 0
-</axis>
-</axes>
-<rules>
-<rule>
-condition  = 1
-type       = eval(sprintf("sv_%s",(split(",",qq{conf(sv_types)}))[counter(sv)]))
-flow       = continue
-</rule>
-<rule>
-condition  = !var(var(type))
-show       = no
-</rule>
-<rule>
-condition  = 1
-value      = 0
-glyph_size = eval(remap_int(var(var(type)),1,10,10,30))
-</rule>
-</rules>
-</plot>
--- a/etc/ticks.conf~	Mon Sep 12 16:23:26 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-
-show_ticks          = yes
-show_tick_labels    = yes
-show_grid = yes
-
-<ticks>
-radius           = dims(ideogram,radius_outer)
-multiplier       = 1e-6
-color            = black
-thickness        = 2p
-
-grid_start = 0.2r
-grid_end   = 0.999r
-grid_color     = lgrey
-grid_thickness = 1p
-
-<tick>
-spacing        = 5u
-size           = 6p
-</tick>
-
-<tick>
-spacing        = 10u
-size           = 10p
-grid = yes
-grid_color = vlgrey
-</tick>
-
-<tick>
-grid = yes
-spacing        = 20u
-size           = 15p
-show_label     = yes
-label_size     = 20p
-label_offset   = 10p
-format         = %d
-</tick>
-
-</ticks>
--- a/etc/track.counter.conf~	Mon Sep 12 16:23:26 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-init_counter           = track:1
-post_increment_counter = track:1
--- a/etc/white.bin.conf~	Mon Sep 12 16:23:26 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-extend_bin = no
-color      = white
-stroke_thickness = 1
-stroke_type = bin