Mercurial > repos > davidvanzessen > argalaxy_tools

changeset 34:f2010de70741 draft

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Uploaded
author davidvanzessen
date Mon, 18 Jan 2016 07:55:31 -0500
parents 2d38d7c1d0d0
children d7580295e13b
files report_clonality/RScript.r report_clonality/circos/circos.conf report_clonality/circos/etc_colors.conf report_clonality/circos/fonts.conf report_clonality/circos/ideogram.conf report_clonality/circos/parse-table.conf report_clonality/circos/ticks.conf report_clonality/r_wrapper.sh
diffstat 8 files changed, 836 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/report_clonality/RScript.r	Wed Jan 13 05:05:32 2016 -0500
+++ b/report_clonality/RScript.r	Mon Jan 18 07:55:31 2016 -0500
@@ -484,10 +484,42 @@
 }
 
 
+# ---------------------- output tables for the circos plots ----------------------
+
+print("Report Clonality - Circos data")
+
+for(smpl in unique(PRODF$Sample)){
+	PRODF.sample = PRODF[PRODF$Sample == smpl,]
+	
+	fltr = PRODF.sample$Top.V.Gene == ""
+	if(sum(fltr) > 0){
+	  PRODF.sample[fltr, "Top.V.Gene"] = "NA"
+	}
+
+	fltr = PRODF.sample$Top.D.Gene == ""
+	if(sum(fltr) > 0){
+	  PRODF.sample[fltr, "Top.D.Gene"] = "NA"
+	}
+
+	fltr = PRODF.sample$Top.J.Gene == ""
+	if(sum(fltr) > 0){
+	  PRODF.sample[fltr, "Top.J.Gene"] = "NA"
+	}
+	
+	v.d = table(PRODF.sample$Top.V.Gene, PRODF.sample$Top.D.Gene)
+	v.j = table(PRODF.sample$Top.V.Gene, PRODF.sample$Top.J.Gene)
+	d.j = table(PRODF.sample$Top.D.Gene, PRODF.sample$Top.J.Gene)
+
+	write.table(v.d, file=paste(smpl, "_VD_circos.txt", sep=""), sep="\t", quote=F, row.names=T, col.names=NA)
+	write.table(v.j, file=paste(smpl, "_VJ_circos.txt", sep=""), sep="\t", quote=F, row.names=T, col.names=NA)
+	write.table(d.j, file=paste(smpl, "_DJ_circos.txt", sep=""), sep="\t", quote=F, row.names=T, col.names=NA)
+}
+
 # ---------------------- calculating the clonality score ----------------------
 
 if("Replicate" %in% colnames(inputdata)) #can only calculate clonality score when replicate information is available
 {
+  print("Report Clonality - Clonality")
   if(clonality_method == "boyd"){
     samples = split(clonalityFrame, clonalityFrame$Sample, drop=T)
    
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_clonality/circos/circos.conf	Mon Jan 18 07:55:31 2016 -0500
@@ -0,0 +1,146 @@
+
+# This is the main configuration file for the Circos tableviewer. This file also
+# depends on colors.conf (definition on basic colors), ideogram.conf (size and spacing of
+# row/cell segments), and ticks.conf (tick spacing and label definitions - these are turned
+# off by default).
+#
+# In addition to these configuration files, the bin/make-conf script creates 
+# colors.conf (colors of row/col segments) and colors_percentile.conf (colors based on
+# cell percentile values). These configuration files are also included via the <<include>> directive.
+#
+# Some elements of the output image are toggled off by default (e.g. row and column highlights, 
+# anchor links to segment labels, tick marks).
+
+<colors>
+<<include etc_colors.conf>>
+<<include colors.conf>>
+#<<include colors_percentile.conf>>
+</colors>
+
+<fonts>
+<<include fonts.conf>>
+</fonts>
+
+<<include ideogram.conf>>
+<<include ticks.conf>>
+
+karyotype = karyotype.txt
+
+<image>
+dir   = .
+file  = circos.png
+24bit = yes
+svg   = no
+png   = yes
+pdf   = no
+# radius of inscribed circle in image
+radius         = 1500p
+background     = white
+# by default angle=0 is at 3 o'clock position
+angle_offset   = -180
+auto_alpha_colors = yes
+auto_alpha_steps  = 5
+</image>
+
+chromosomes_units              = 10
+chromosomes_display_default    = yes
+chromosomes_order_by_karyotype = yes
+
+<highlights>
+
+show = yes
+
+<highlight>
+show = no
+file = data/row.txt
+r0 = 1r+200p
+r1 = 1r+220p
+stroke_color = black
+stroke_thickness = 2
+</highlight>
+
+<highlight>
+show = no
+file = data/col.txt
+r0 = 1r+230p
+r1 = 1r+250p
+stroke_color = black
+stroke_thickness = 2
+</highlight>
+
+<highlight>
+show = no
+file = data/all.txt
+r0 = 1r+10p
+r1 = 1r+35p
+stroke_color = black
+stroke_thickness = 2
+</highlight>
+
+</highlights>
+
+<plots>
+
+<plot>
+type = text
+file = data/segmentlabel.txt
+label_font = condensedbold
+color = black
+label_size = 30p
+r0   = 1r+50p
+r1   = 1r+500p
+rpadding = 0p
+padding = 0p
+
+show_links     = no
+link_dims      = 0p,10p,32p,10p,5p
+link_thickness = 3p
+link_color     = black
+
+label_snuggle             = no
+# shift label up to its height in pixels in the angular direction
+max_snuggle_distance      = 2r
+snuggle_sampling          = 2
+snuggle_tolerance         = 0.25r
+
+</plot>
+
+</plots>
+
+<links>
+
+<link cellvalues>
+ribbon        = yes
+flat          = yes
+file          = data/cells.txt
+bezier_radius = 0.0r
+radius        = 0.999r-15p
+thickness     = 1
+color         = grey
+stroke_color     = black
+stroke_thickness = 1
+<rules>
+
+<rule>
+importance = 95
+condition  = 1
+radius1    = 0.999r+2p
+flow       = continue
+</rule>
+
+</rules>
+
+</link>
+
+</links>
+
+anglestep       = 0.5
+minslicestep    = 10
+beziersamples   = 40
+debug           = no
+warnings        = no
+imagemap        = no
+
+units_ok = bupr
+units_nounit = n
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_clonality/circos/etc_colors.conf	Mon Jan 18 07:55:31 2016 -0500
@@ -0,0 +1,142 @@
+# RGB color definition. Colors are refered to within configuration files
+# by their name. In order to use a color, you must define it here. 
+# 
+# e.g. if you really must use 'bisque', then add
+#
+# bisque = 255,228,196
+#
+# Many useful colors are already defined. In general, given a HUE, these
+# colors are defined
+#
+# vlHUE (very light HUE, e.g. vlred)
+# lHUE  (light HUE, e.g. red)
+# HUE   (e.g. red)
+# dHUE  (dark HUE, e.g. dred)
+#
+# In addition to hues, two other color groups are defined. 
+#
+# - cytogenetic band colors (e.g. gposNNN, acen, stalk, etc.) which
+#   correspond to colors on ideogram bands
+# - UCSC chromosome color palette (e.g. chrNN, chrUn, chrNA)
+
+optblue   = 55,133,221
+optgreen  = 55,221,125
+optyellow = 221,215,55
+optorange = 221,164,55
+optred    = 221,55,55
+optviolet = 145,55,221
+optpurple = 219,55,221
+
+white     = 255,255,255
+vvvvlgrey = 250,250,250
+vvvlgrey  = 240,240,240
+vvlgrey   = 230,230,230
+vlgrey    = 220,220,220
+lgrey     = 210,210,210
+grey      = 200,200,200
+dgrey     = 170,170,170
+vdgrey    = 140,140,140
+vvdgrey   = 100,100,100
+vvvdgrey  = 70,70,70
+vvvvdgrey = 40,40,40
+black     = 0,0,0
+
+vlred   = 255,193,200
+lred    = 255,122,137
+red     = 247,42,66
+dred    = 205,51,69
+
+vlgreen = 204,255,218
+lgreen  = 128,255,164
+green   = 51,204,94
+dgreen  = 38,153,71
+
+vlblue  = 128,176,255
+lblue   = 64,137,255
+blue    = 54,116,217
+dblue   = 38,82,153
+
+vlpurple= 242,128,255
+lpurple = 236,64,255
+purple  = 189,51,204
+dpurple = 118,32,128
+
+vlyellow = 255,253,202
+lyellow  = 255,252,150
+yellow   = 255,255,0
+dyellow  = 191,186,48
+
+lime     = 186,255,0
+
+vlorange = 255,228,193
+lorange  = 255,187,110
+orange   = 255,136,0
+dorange  = 221,143,55
+
+# karyotype colors
+
+gpos100 = 0,0,0
+gpos    = 0,0,0
+gpos75  = 130,130,130
+gpos66  = 160,160,160
+gpos50  = 200,200,200
+gpos33  = 210,210,210
+gpos25  = 200,200,200
+gvar    = 220,220,220
+gneg    = 255,255,255
+acen    = 217,47,39
+stalk   = 100,127,164
+
+# others
+
+select = 135,177,255
+
+# new york times cmyk-safe
+
+# roygbiv - normal
+nyt_blue   = 104,152,178
+nyt_green  = 137,129,96
+nyt_yellow = 241,221,117
+nyt_orange = 230,146,57
+nyt_red    = 217,47,39
+
+# chromosome color map (UCSC) 
+
+chr1 = 153,102,0
+chr2 = 102,102,0
+chr3 = 153,153,30
+chr4 = 204,0,0
+chr5 = 255,0,0
+chr6 = 255,0,204
+chr7 = 255,204,204
+chr8 = 255,153,0
+chr9 = 255,204,0
+chr10 = 255,255,0
+chr11 = 204,255,0
+chr12 = 0,255,0
+chr13 = 53,128,0
+chr14 = 0,0,204
+chr15 = 102,153,255
+chr16 = 153,204,255
+chr17 = 0,255,255
+chr18 = 204,255,255
+chr19 = 153,0,204
+chr20 = 204,51,255
+chr21 = 204,153,255
+chr22 = 102,102,102
+chr23 = 153,153,153
+chrX  = 153,153,153
+chr24 = 204,204,204
+chrY = 204,204,204
+chrM = 204,204,153
+chr0 = 204,204,153
+chrUn = 121,204,61
+chrNA = 255,255,255
+
+
+
+
+
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_clonality/circos/fonts.conf	Mon Jan 18 07:55:31 2016 -0500
@@ -0,0 +1,8 @@
+
+default       = fonts/LTe50046.ttf
+normal        = fonts/LTe50046.ttf
+bold          = fonts/LTe50048.ttf
+condensed     = fonts/LTe50050.ttf
+condensedbold = fonts/LTe50054.ttf
+mono          = fonts/pragmata.ttf
+glyph         = fonts/wingding.ttf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_clonality/circos/ideogram.conf	Mon Jan 18 07:55:31 2016 -0500
@@ -0,0 +1,37 @@
+
+<ideogram>
+
+<spacing>
+
+default = 0.0025r
+
+</spacing>
+
+thickness        = 50p
+stroke_thickness = 0
+# ideogram border color
+stroke_color     = black
+fill             = yes
+# the default chromosome color is set here and any value
+# defined in the karyotype file overrides it
+fill_color       = black
+
+# fractional radius position of chromosome ideogram within image
+radius         = 0.85r
+show_label     = no
+label_font     = condensedbold
+label_radius   = 0.99r
+label_size     = 36
+
+# cytogenetic bands
+band_stroke_thickness = 2
+
+# show_bands determines whether the outline of cytogenetic bands
+# will be seen
+show_bands            = no
+# in order to fill the bands with the color defined in the karyotype
+# file you must set fill_bands
+fill_bands            = yes
+
+</ideogram>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_clonality/circos/parse-table.conf	Mon Jan 18 07:55:31 2016 -0500
@@ -0,0 +1,391 @@
+
+################################################################
+#
+# This is a fairly complicated configuration file. Take your time in
+# experimenting and adjust one thing at a time :)
+#
+################################################################
+
+max_col_num = 200
+max_row_num = 200
+
+# skip this many rows before reading in header and data
+skip_rows        = 0
+
+# is there a header line that identifies the columns?
+header           = yes
+
+# is there a row that specifies the order of columns in the image?
+# - if so, this must be the first line of the header
+# - if the line exists (col_order_row=yes), employ the use_col_order_row to toggle whether it is used
+col_order_row     = no
+use_col_order_row = no
+
+# is there a row that specifies the size of columns in the image?
+# - if so, this must be the next line of the header
+# - if the line exists (col_size_row=yes), employ the use_col_size_row to toggle whether it is used
+col_size_row     = no
+use_col_size_row = no
+
+# is there a row that specifies the color of each column segment in the image?
+# - if so, this must be the next line of the header
+# - if the line exists (col_color_row=yes), employ the use_col_color_row to toggle whether it is used
+col_color_row     = no
+use_col_color_row = no
+
+# is there a column that specifies the order of rows in the image?
+# - if so, this must be the first column
+# - if the line exists (row_order_col=yes), employ the use_row_order_col to toggle whether it is used
+row_order_col     = no
+use_row_order_col = no
+
+# is there a column that specifies the color of each row segment in the image?
+# - if so, this must be the second column
+# - if the line exists (row_color_col=yes), employ the use_row_color_col to toggle whether it is used
+row_color_col     = no
+use_row_color_col = no
+
+# if you do not have a column/row that explicitly defines order
+# of segments in the image, you can set this here. Use one (or more) of 
+# these values to specify how segments should be ordered.
+# - row_major (row segments first, then column)
+# - col_major (col segments first, then row)
+# - ascii     (asciibetic order)
+# - row_size  (total of rows for the segment - useful if the segment has both row and column contributions)
+# - col_size  (total of colums for the segment - useful if the segment has both row and column contributions)
+# - row_to_col_ratio (ratio of total of rows to columns for the segment)
+# - col_to_row_ratio (ratio of total of rows to columns for the segment)
+# - size_asc  (size, in ascending order)
+# - size_desc (size, in descending order)
+
+#segment_order = row_to_col_ratio,size_desc # col_major,size_desc
+#segment_order = size_desc
+segment_order = row_major,size_desc
+#segment_order = ascii
+#segment_order = file:etc/order-by-table-remapped.txt
+#segment_order  = size_desc,row_to_col_ratio
+segment_color_order = row_major,size_desc
+
+# values for segments can be normalized if the use_segment_normalization is set to yes
+use_segment_normalization = no
+
+# the normalization function can be one of the following, and is applied to
+# all values that correspond to the segment's label
+# total - sum of cell values for the segment label (row and col)
+# average - average of cell values for the segment label (row and col)
+# row_total, row_average - sum or average for cell values for the segment row
+# col_total, col_average - sum or average for cell values for the segment col
+# row_size, col_size, total_size - based on the optional size column (see col_size_row and row_size_col above)
+# VALUE - segments are scaled to a constant VALUE (e.g. 1000)
+segment_normalization_function = 1000
+
+# normalization can be performed by either altering the actual data values or
+# by applying a visual scaling of the segments. When 'value' is used, the data
+# is changed. When 'visual' is used, then a chromosomes_scale line is reported
+# by this script which you must include in circos.conf for the scaling to be applied
+segment_normalization_scheme   = value
+
+################################################################
+# placement of cell ribbons on row/column segments
+# 
+# for segments that share both column and row ribbons, the
+# order of ribbon position can be adjusted with placement_order
+
+placement_order = row,col # col,row or row,col
+
+# within the row/column ribbon bundle for each segment, 
+# ribbon_bundle_order determines how the ribbons will be
+# ordered
+# - size   - by value of the cell
+# - ascii  - sorted by destination label
+# - native - sorted by order of destination segment
+
+ribbon_bundle_order = native # size, ascii, native
+
+# reverse the position of links in table/row segments?
+
+reverse_rows    = no
+reverse_columns = no
+
+# values for cells with the same row/column name can be treated
+# independently. You can
+# show - show these cells and not filter them at all
+# hide - hide these cells from the image, but not resize the row/columns
+# remove - entirely remove these cells from the data set (equivalent to setting cells to missing value)
+intra_cell_handling = show
+
+# ribbon layering - order in which the ribbons are drawn on the image
+# size_asc  - ascending by ribbon size (small ribbons drawn first, therefore large ribbons will be at front)
+# size_desc - descending by ribbon size (large ribbons drawn first, therefore small ribbons will be at front)
+
+ribbon_layer_order = size_asc
+
+# if both (A,B)=x and (B,A)=y cells exist, you can choose to have the ribbon
+# ends sized variably so that ribbon at A has width x and at B has width y
+
+ribbon_variable = no
+ribbon_variable_intra_collapse = yes
+
+################################################################
+# cell value mapping allows you to remap the cell values using
+# any Perl expression that uses X as the cell value. For example,
+#
+# cell_remap_formula = log(X)
+#                    = sqrt(X)
+#                    = X/10
+#                    = X ? log(X) : 0
+#
+# This remapping takes place before any filters or scaling is applied. Its effect
+# is the same as remapping the cell values in the input file.
+
+use_cell_remap     = no
+cell_remap_formula = round(10*X)
+
+################################################################
+# scale your values with a power rule (useful if the range of values
+# is very large) to
+# - atten_large: attenuate large values and maintain visibility
+#   of ribbons corresponding to small values, or
+# - atten_small: attenuate small values to increase visibility
+#   of ribbons corresponding to large values
+#
+# given a value, v, and a maximum, m
+#
+# atten_small:
+#
+# v_new = m * ( exp(scale_factor * v / m) - 1 ) / ( exp(scale_factor) - 1 )
+#
+# atten_large:
+#
+# v_new = m * ( log(scale_factor * v ) ) / ( log(scale_factor * m ) )
+# 
+# essentially the values are remapped to a log-type scale 
+# with the range 0..m
+
+use_scaling    = no
+scaling_type   = atten_large
+scale_factor   = 1
+
+blank_means_missing = no
+missing_cell_value = -
+
+################################################################
+# Value cutoffs for cell values and ribbon formatting.
+#
+# You can toggle the visibility of ribbons for cells outside
+# a min/max range. You can define one or more of these cutoffs.
+# The cutoffs are applied to unscaled cell values.
+
+#cell_min_value      = 10
+#cell_min_percentile = 10
+#cell_max_value      = 100
+#cell_max_percentile = 100
+
+# For cell values that do not pass the min/max filters above,
+# you can specify whether they are hidden or removed. If the
+# parameter is not defined, "hide" will be assumed.
+# hide - cell values won't be shown, but row/col will not be resized
+# remove - entirely remove these cells from the data set (equivalent to setting cells to missing value)
+
+cutoff_cell_handling = hide
+
+# The color of ribbons is by default the color of the row segment from
+# which they originate. The block below allows you to remap the color
+# of the ribbons based on cell percentile values. There are two ways
+# to remap colors
+# 
+# - color_remap=yes, color_autoremap=no
+#   Uses <percentile> blocks to define the percentile values and associated
+#   color/stroke_color characteristics for ribbons. Percentile value defined
+#   in the block (e.g. <percentile 55>) is the max percentile value for
+#   cells associated with this block.
+# - color_remap=yes, color_autoremap=yes
+#   Uses colors associated with each percentile window of size
+#   percentile_sampling for each cell
+
+<linkcolor>
+color_source       = row
+percentile_source  = larger
+color_transparency = 1
+color_remap        = yes
+color_autoremap    = no
+
+<percentile 50>
+color = dgrey
+transparency = 5
+</percentile>
+
+<percentile 60>
+color = dgrey
+transparency = 5
+</percentile>
+
+<percentile 70>
+transparency = 1
+</percentile>
+
+<percentile 80>
+transparency = 1
+</percentile>
+
+<percentile 90>
+transparency = 1
+stroke_color = black
+stroke_thickness = 1p
+</percentile>
+
+<percentile 100>
+transparency = 1
+stroke_color = black
+stroke_thickness = 3p
+</percentile>
+
+</linkcolor>
+
+<linkparam>
+color = vdgrey
+#stroke_color = black
+#stroke_thickness = 1p
+</linkparam>
+
+# If you are using color_autoremap=yes above, then
+# define the percentile sampling window and 
+# the start/end HSV color values. Percentile window
+# colors are interpolated between this HSV pair.
+#
+# HSV = (hue saturation value) 
+# hue=(0..360) saturation=(0..1) value=(0..1) 
+
+percentile_sampling = 5
+
+# count - percentile based on counts
+# value - percentile based on value
+
+percentile_method = count
+
+# use all values or only unique values when
+# calculating percentiles
+percentile_unique_only = yes
+
+# use a function, f(X), to remap cell values when calculating percentiles
+# for the purpose of color mapping. This allows you to apply a remapping to how
+# colors are calculated, without actually changing the values. The remap
+# applies only if percentile_method=value
+
+# percentile_remap = sqrt(X)
+
+# Which cell value set to use for percentile color mapping
+# raw - original values
+# filtered - values that pass min/max filters
+# scaled - filtered values that have been scaled if use_scaling is set
+percentile_data_domain = raw
+
+<colors>
+h0 = 0
+s0 = 1
+v0 = 1
+h1 = 300
+s1 = 1
+v1 = 1
+</colors>
+
+# You can control the color and stroke of ribbons for each
+# quartile (q1, q2, q3, q4). Any values defined here will
+# overwrite colors determined by remapping. 
+#
+# For example, if you have a lot of cells and wish to attenuate
+# the visibility of ribbons associated with small values, you can
+# set cell_q1_color=vvlgrey,cell_q1_nostroke=yes to fade the
+# ribbons into the background.
+
+#cell_q1_color    = vvlgrey
+#cell_q2_color    = vlgrey
+#cell_q3_color    = lgrey
+#cell_q4_color    = red
+#cell_q1_nostroke = yes
+#cell_q2_nostroke = yes
+#cell_q3_nostroke = yes
+#cell_q4_nostroke = yes
+
+# cell value multiplier, required when all data is small (e.g. <1), in which
+# case set the multiplier to something like 1000 because Circos
+# works only with integer scales
+
+data_mult = 1
+
+################################################################
+# Segment labels can be optionally set to a size that is
+# proportional to the size of the segment. Set min/max size
+# values here. If this line is commented out, then the label
+# size is determined by the circos.conf file used to draw the image
+
+#segment_label_size_range       = 60,60
+
+# progression controls how fast the label size changes from
+# min to max (larger value of progression means values close to max
+# are achieved for smaller segments)
+
+segment_label_size_progression = 4
+
+segment_label_uppercase = no
+
+################################################################
+# Segment colors can be specified in the data file (in this
+# case use row_color_col and col_color_row), otherwise colors
+# are interpolated within an HSV range. Color interpolation can be
+# done in two ways: based on segment index (interpolation steps through
+# colors uniformly for each segment) and total size (interpolation
+# steps through colors in proportion to segment size).
+
+<segment_colors>
+interpolate_type = size # size or count
+h0 = 0
+s0 = 0.8
+v0 = 0.9
+h1 = 300
+s1 = 0.8
+v1 = 0.9
+</segment_colors>
+
+################################################################
+# Shorten the labels of segments. Specify whether to do this
+# with shorten_text=yes|no parameter and provide regular
+# expressions in string_replace which define the text to
+# replace. 
+
+shorten_text = yes
+
+<string_replace>
+IGH = 
+</string_replace>
+
+# exit on any error
+strict_sanity = yes
+
+################################################################
+# if the segment_prefix is set, then rows and columns will be
+# renamed to internal fields segment_prefix + DIGIT
+
+#segment_prefix  = id
+color_prefix = color
+
+################################################################
+# Delimiters
+
+# field delimiter regular expression
+# if this is not defined, any whitespace will be considered a delimiter
+field_delim = \s
+
+# collapse adjacent delimiters?
+field_delim_collapse = yes
+
+# remove any leading space in the input file
+# by default, this is on - if you set this to "no", make sure that you don't have any leading spaces in your table!
+strip_leading_space = yes
+
+# remove quotes and thousand separators - concatenate characters to remove
+#
+# e.g. to remove characters a b c set remove_cell_rx=abc
+# e.g. to remove characters " ' , set remove_cell_rx="',
+remove_cell_rx = "',
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_clonality/circos/ticks.conf	Mon Jan 18 07:55:31 2016 -0500
@@ -0,0 +1,65 @@
+
+show_ticks          = no
+show_tick_labels    = no
+chrticklabels       = yes
+chrticklabelfont    = default
+
+grid_start         = dims(ideogram,radius_inner)-0.5r
+grid_end           = dims(ideogram,radius_outer)+100
+
+<ticks>
+skip_first_label     = no
+skip_last_label      = no
+radius               = dims(ideogram,radius_outer)
+label_offset     = 0p
+color = black
+
+<tick>
+spacing        = 5u
+spacing_type   = relative
+rspacing       = 0.1
+size           = 3p
+thickness      = 2p
+color          = dgrey
+show_label     = yes
+label_size     = 16p
+label_offset   = 3p
+label_relative = yes
+format         = %d
+grid           = yes
+grid_color     = dgrey
+grid_thickness = 1p
+suffix = %
+rmultiplier = 100
+offset = 40p
+</tick>
+
+<tick>
+spacing        = 50u
+size           = 3p
+thickness      = 2p
+color          = black
+show_label     = yes
+label_size     = 12p
+label_offset   = 3p
+format         = %d
+grid           = yes
+grid_color     = dgrey
+grid_thickness = 1p
+</tick>
+
+<tick>
+spacing        = 10u
+size           = 2p
+thickness      = 1p
+color          = black
+show_label     = no
+label_size     = 12p
+label_offset   = 3p
+format         = %d
+grid           = yes
+grid_color     = dgrey
+grid_thickness = 1p
+</tick>
+
+</ticks>
--- a/report_clonality/r_wrapper.sh	Wed Jan 13 05:05:32 2016 -0500
+++ b/report_clonality/r_wrapper.sh	Mon Jan 18 07:55:31 2016 -0500
@@ -31,6 +31,7 @@
 cp $dir/script.js $outputDir
 cp $dir/jquery-1.11.0.min.js $outputDir
 samples=`cat $outputDir/samples.txt`
+CIRCOSTOOLS="/home/galaxy/Downloads/circos-master/tools"
 echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)<br />" > $2
 echo "<table border = 1>" >> $2
 echo "<thead><tr><th>Sample/Replicate</th><th>All</th><th>Productive</th><th>Unique Productive</th><th>Unproductive</th><th>Unique Unproductive</th></tr></thead>" >> $2
@@ -47,8 +48,18 @@
 
 echo "productive_counting.txt"
 echo "<html><head><title>Report on:" >> $outputFile
+
+mkdir $outputDir/circos
+cp $dir/circos/* $outputDir/circos/
 for sample in $samples; do
 	echo " $sample" >> $outputFile
+	
+		circos_file="$outputDir/${sample}_VD_circos.txt"
+		echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
+		#echo -n "labels" > $outputDir/tmp.txt
+		#cat ${circos_file} >> $outputDir/tmp.txt
+		#mv $outputDir/tmp.txt ${circos_file}
+		#cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/; /home/galaxy/Downloads/circos-master/bin/circos -param karyotype=$outputDir/circos/karyotype.txt -conf $dir/circos/circos.conf 2>&1
 done
 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile
 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile
@@ -90,7 +101,7 @@
 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
 echo "$hasReplicateColumn"
 #if its a 'new' merged file with replicate info
-if [[ "$hasReplicateColumn" == "Yes" && "$clonalType" != "none" ]] ; then
+if [[ "$hasReplicateColumn" == "Yes" ]] ; then
 	echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile
 	for sample in $samples; do
 		echo "${clonality_method}"
@@ -137,9 +148,10 @@
 	echo "</div></div>" >> $outputFile
 fi
 
-hasJunctionData="$(if head -n 1 $inputFile | grep -qE '3V.REGION.trimmed.nt.nb'; then echo 'Yes'; else echo 'No'; fi)"
+#hasJunctionData="$(if head -n 1 $inputFile | grep -qE '3V.REGION.trimmed.nt.nb'; then echo 'Yes'; else echo 'No'; fi)"
 
-if [[ "$hasJunctionData" == "Yes" ]] ; then
+#if [[ "$hasJunctionData" == "Yes" ]] ; then
+if [ -a "$outputDir/junctionAnalysisProd.csv" ] ; then
 	echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile
 	echo "<table border='1' id='junction_table'> <caption>Productive</caption><thead><tr><th>Sample</th><th>count</th><th>VH.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.DH</th><th>DH.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.JH</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile
 	while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP