figure 4 - recip inv

sv-linx/src/main/resources/figure4/SAMPLE.RECIP_INV_DEL.circos.conf

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+# /Users/jon/hmf/tools/circos-0.69-6/bin/circos -nosvg -conf /Users/jon/hmf/repos/hmftools/sv-linx/src/main/resources/figure4/SAMPLE.RECIP_INV_DEL.circos.conf -outputdir /Users/jon/hmf/analysis/fusions/plot -outputfile SAMPLE.RECIP_INV_DEL.png
+
+<<include etc/colors_fonts_patterns.conf>>
+
+show_ticks          = no
+show_tick_labels    = no
+
+<ideogram>
+    <spacing>
+        default = 6u
+    </spacing>
+
+    # Ideogram position, fill and outline
+    radius           = 0.9r
+    thickness        = 50p
+    fill             = yes
+    stroke_color     = dgrey
+    stroke_thickness = 2p
+
+    show_label       = no
+    label_font       = default
+    label_radius     = (dims(ideogram,radius_inner)+dims(ideogram,radius_outer))/2-15
+    label_size       = 30
+    label_parallel   = yes
+    label_case       = upper
+    label_format     = eval( var(chr) =~ /hs([6]|[9])$/ ? var(label) . ".": var(label) )
+
+    chromosome = -hs18
+
+</ideogram>
+
+<highlights>
+    z = 0
+
+    <highlight>
+		file = SAMPLE.RECIP_INV_DEL.segment.circos
+        <rules>
+            <rule>
+                condition = var(value) == 0
+                show = no
+            </rule>
+        </rules>
+    </highlight>
+
+
+
+</highlights>
+
+<image>
+	angle_offset* = -87
+
+    dir   = .
+
+    # radius of inscribed circle in image
+    radius         = 1500p
+
+    # by default angle=0 is at 3 o'clock position
+    angle_offset      = -90
+
+    auto_alpha_colors = yes
+    auto_alpha_steps  = 5
+    background = white
+</image>
+
+karyotype = SAMPLE.SGL.karyotype.circos
+
+chromosomes_units           = 1
+chromosomes_display_default = yes
+
+# Default is to clip the data to proximity min/max.
+<plots>
+
+
+	# -----------------------------------------------------------
+	# Background
+	<plot>
+		r0   = 0.70r
+		r1   = 0.95r
+
+		<backgrounds>
+			<background>
+				color = vlpurple_a5
+			</background>
+		</backgrounds>
+
+		<axes>
+			<axis>
+				color     = lpurple
+				thickness = 1
+				position  = 0.25r,0.75r
+			</axis>
+		</axes>
+
+	</plot>
+
+
+	# -----------------------------------------------------------
+	# CopyNumber Gain (Green)
+	<plot>
+		type = histogram
+		file = SAMPLE.RECIP_INV_DEL.cna.circos
+		r0   = 0.40r
+		r1   = 0.65r
+		min  = 0
+		max  = 2
+		glyph = circle
+		glyph_size = 8
+		color = green
+		fill_color = green
+
+		<axes>
+			<axis>
+				color     = lgreen
+				thickness = 1
+				position  = 0.5r,1.0r
+			</axis>
+		</axes>
+
+		<backgrounds>
+			<background>
+				color = vlgreen_a5
+			</background>
+		</backgrounds>
+
+	</plot>
+
+
+	# -----------------------------------------------------------
+	# CopyNumber Loss (Red)
+	<plot>
+		type = histogram
+		file = SAMPLE.RECIP_INV_DEL.cna.circos
+		r0   = 0.15r
+		r1   = 0.40r
+		min  = -2
+		max  = 0
+		color = red
+		glyph = circle
+		glyph_size = 8
+		fill_color = red
+
+		<axes>
+			<axis>
+				color     = lred
+				thickness = 1
+				spacing   = 0.5r
+			</axis>
+		</axes>
+
+		<backgrounds>
+			<background>
+				color = vlred_a5
+			</background>
+		</backgrounds>
+
+	</plot>
+
+
+	# -----------------------------------------------------------
+	# Scatter
+	<plot>
+		type             = scatter
+		file             = SAMPLE.RECIP_INV_DEL.scatter.circos
+
+		r0   = 0.70r
+		r1   = 0.95r
+
+        glyph            = circle
+        glyph_size       = 20
+        color            = red
+        stroke_color     = dred
+        stroke_thickness = 0
+        orientation      = out
+
+        min  = 0
+        max = 4
+
+	</plot>
+
+	# -----------------------------------------------------------
+	# Connectors
+    <plot>
+
+        type = connector
+        file = SAMPLE.RECIP_INV_DEL.connector.circos
+
+        r0	=	0.175r
+        connector_dims = 0.0,0.3,0.4,0.3,0
+
+        thickness = 25
+        color     = red
+    </plot>
+
+</plots>
+
+<links>
+    <link>
+        file          = SAMPLE.RECIP_INV_DEL.link.circos
+        color         = red
+        radius        = 0.175r
+        thickness     = 25
+    </link>
+</links>
+
+<<include etc/housekeeping.conf>>
+
+<colors>
+    chr1 = 128,125,186
+    chr2 = 145,142,179
+    chr3 = 161,159,173
+    chr4 = 179,176,166
+    chr5 = 196,193,160
+    chr6 = 213,210,153
+
+    chr7 = 230,228,147
+    chr8 = 202,218,138
+    chr9 = 175,209,129
+    chr10 = 147,199,120
+    chr11 = 120,190,111
+    chr12 = 92,180,102
+
+    chr13 = 65,171,93
+    chr14 = 65,166,110
+    chr15 = 65,162,128
+    chr16 = 65,158,145
+    chr17 = 65,154,163
+    chr18 = 65,150,180
+
+    chr19 = 66,146,198
+    chr20 = 76,142,196
+    chr21 = 86,139,194
+    chr22 = 97,135,192
+    chrX = 107,132,190
+    chrY = 117,128,188
+</colors>

sv-linx/src/main/resources/figure4/SAMPLE.RECIP_INV_DEL.cna.circos

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+hs16	60	90	-1
+hs16	90	240	0
+hs16	240	300	-1
+

sv-linx/src/main/resources/figure4/SAMPLE.RECIP_INV_DEL.connector.circos

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+hs16	60	60	r1=0.7625r,color=(106,61,154,0.7)
+hs16	90	90	r1=0.8875r,color=(106,61,154,0.7)
+hs16	240	240	r1=0.8875r,color=(106,61,154,0.7)
+hs16	300	300	r1=0.8875r,color=(106,61,154,0.7)

sv-linx/src/main/resources/figure4/SAMPLE.RECIP_INV_DEL.link.circos

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+hs16	90	90	hs16	300	300	color=(106,61,154,0.7)
+hs16	60	60	hs16	240	240	color=(106,61,154,0.7)

sv-linx/src/main/resources/figure4/SAMPLE.RECIP_INV_DEL.scatter.circos

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+hs16	5	5	1	color=(106,61,154),glyph=square,glyph_size=90
+hs16	5	5	1	color=white,glyph=square,glyph_size=60
+hs16	60	60	1	color=(106,61,154),glyph=circle,glyph_size=90
+hs16	90	90	3	color=(106,61,154),glyph=circle,glyph_size=90
+hs16	240	240	3	color=(106,61,154),glyph=circle,glyph_size=90
+hs16	300	300	3	color=(106,61,154),glyph=circle,glyph_size=90
+hs16	356	356	3	color=(106,61,154),glyph=square,glyph_size=90

sv-linx/src/main/resources/figure4/SAMPLE.RECIP_INV_DEL.segment.circos

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+hs16	5	60	1	fill_color=(106,61,154),r0=0.7625r,r1=0.7625r+25p
+hs16	90	240	2	fill_color=(106,61,154),r0=0.8875r,r1=0.8875r+25p
+hs16	300	356	1	fill_color=(106,61,154),r0=0.8875r,r1=0.8875r+25p

sv-linx/src/main/resources/figure4/SAMPLE.SGL.karyotype.circos

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+chr - hs16 16 1 360 chr8