comparison report_clonality/circos/parse-table.conf @ 5:bcec7bb4e089 draft

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author davidvanzessen
date Mon, 12 Dec 2016 05:22:57 -0500
parents afe85eb6572e
children 124b7fd92a3e
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1
2 ################################################################
3 #
4 # This is a fairly complicated configuration file. Take your time in
5 # experimenting and adjust one thing at a time :)
6 #
7 ################################################################
8
9 max_col_num = 200
10 max_row_num = 200
11
12 # skip this many rows before reading in header and data
13 skip_rows = 0
14
15 # is there a header line that identifies the columns?
16 header = yes
17
18 # is there a row that specifies the order of columns in the image?
19 # - if so, this must be the first line of the header
20 # - if the line exists (col_order_row=yes), employ the use_col_order_row to toggle whether it is used
21 col_order_row = no
22 use_col_order_row = no
23
24 # is there a row that specifies the size of columns in the image?
25 # - if so, this must be the next line of the header
26 # - if the line exists (col_size_row=yes), employ the use_col_size_row to toggle whether it is used
27 col_size_row = no
28 use_col_size_row = no
29
30 # is there a row that specifies the color of each column segment in the image?
31 # - if so, this must be the next line of the header
32 # - if the line exists (col_color_row=yes), employ the use_col_color_row to toggle whether it is used
33 col_color_row = no
34 use_col_color_row = no
35
36 # is there a column that specifies the order of rows in the image?
37 # - if so, this must be the first column
38 # - if the line exists (row_order_col=yes), employ the use_row_order_col to toggle whether it is used
39 row_order_col = no
40 use_row_order_col = no
41
42 # is there a column that specifies the color of each row segment in the image?
43 # - if so, this must be the second column
44 # - if the line exists (row_color_col=yes), employ the use_row_color_col to toggle whether it is used
45 row_color_col = no
46 use_row_color_col = no
47
48 # if you do not have a column/row that explicitly defines order
49 # of segments in the image, you can set this here. Use one (or more) of
50 # these values to specify how segments should be ordered.
51 # - row_major (row segments first, then column)
52 # - col_major (col segments first, then row)
53 # - ascii (asciibetic order)
54 # - row_size (total of rows for the segment - useful if the segment has both row and column contributions)
55 # - col_size (total of colums for the segment - useful if the segment has both row and column contributions)
56 # - row_to_col_ratio (ratio of total of rows to columns for the segment)
57 # - col_to_row_ratio (ratio of total of rows to columns for the segment)
58 # - size_asc (size, in ascending order)
59 # - size_desc (size, in descending order)
60
61 #segment_order = row_to_col_ratio,size_desc # col_major,size_desc
62 #segment_order = size_desc
63 segment_order = row_major,size_desc
64 #segment_order = ascii
65 #segment_order = file:etc/order-by-table-remapped.txt
66 #segment_order = size_desc,row_to_col_ratio
67 segment_color_order = row_major,size_desc
68
69 # values for segments can be normalized if the use_segment_normalization is set to yes
70 use_segment_normalization = no
71
72 # the normalization function can be one of the following, and is applied to
73 # all values that correspond to the segment's label
74 # total - sum of cell values for the segment label (row and col)
75 # average - average of cell values for the segment label (row and col)
76 # row_total, row_average - sum or average for cell values for the segment row
77 # col_total, col_average - sum or average for cell values for the segment col
78 # row_size, col_size, total_size - based on the optional size column (see col_size_row and row_size_col above)
79 # VALUE - segments are scaled to a constant VALUE (e.g. 1000)
80 segment_normalization_function = 1000
81
82 # normalization can be performed by either altering the actual data values or
83 # by applying a visual scaling of the segments. When 'value' is used, the data
84 # is changed. When 'visual' is used, then a chromosomes_scale line is reported
85 # by this script which you must include in circos.conf for the scaling to be applied
86 segment_normalization_scheme = value
87
88 ################################################################
89 # placement of cell ribbons on row/column segments
90 #
91 # for segments that share both column and row ribbons, the
92 # order of ribbon position can be adjusted with placement_order
93
94 placement_order = row,col # col,row or row,col
95
96 # within the row/column ribbon bundle for each segment,
97 # ribbon_bundle_order determines how the ribbons will be
98 # ordered
99 # - size - by value of the cell
100 # - ascii - sorted by destination label
101 # - native - sorted by order of destination segment
102
103 ribbon_bundle_order = native # size, ascii, native
104
105 # reverse the position of links in table/row segments?
106
107 reverse_rows = no
108 reverse_columns = no
109
110 # values for cells with the same row/column name can be treated
111 # independently. You can
112 # show - show these cells and not filter them at all
113 # hide - hide these cells from the image, but not resize the row/columns
114 # remove - entirely remove these cells from the data set (equivalent to setting cells to missing value)
115 intra_cell_handling = show
116
117 # ribbon layering - order in which the ribbons are drawn on the image
118 # size_asc - ascending by ribbon size (small ribbons drawn first, therefore large ribbons will be at front)
119 # size_desc - descending by ribbon size (large ribbons drawn first, therefore small ribbons will be at front)
120
121 ribbon_layer_order = size_asc
122
123 # if both (A,B)=x and (B,A)=y cells exist, you can choose to have the ribbon
124 # ends sized variably so that ribbon at A has width x and at B has width y
125
126 ribbon_variable = no
127 ribbon_variable_intra_collapse = yes
128
129 ################################################################
130 # cell value mapping allows you to remap the cell values using
131 # any Perl expression that uses X as the cell value. For example,
132 #
133 # cell_remap_formula = log(X)
134 # = sqrt(X)
135 # = X/10
136 # = X ? log(X) : 0
137 #
138 # This remapping takes place before any filters or scaling is applied. Its effect
139 # is the same as remapping the cell values in the input file.
140
141 use_cell_remap = no
142 cell_remap_formula = round(10*X)
143
144 ################################################################
145 # scale your values with a power rule (useful if the range of values
146 # is very large) to
147 # - atten_large: attenuate large values and maintain visibility
148 # of ribbons corresponding to small values, or
149 # - atten_small: attenuate small values to increase visibility
150 # of ribbons corresponding to large values
151 #
152 # given a value, v, and a maximum, m
153 #
154 # atten_small:
155 #
156 # v_new = m * ( exp(scale_factor * v / m) - 1 ) / ( exp(scale_factor) - 1 )
157 #
158 # atten_large:
159 #
160 # v_new = m * ( log(scale_factor * v ) ) / ( log(scale_factor * m ) )
161 #
162 # essentially the values are remapped to a log-type scale
163 # with the range 0..m
164
165 use_scaling = no
166 scaling_type = atten_large
167 scale_factor = 1
168
169 blank_means_missing = no
170 missing_cell_value = -
171
172 ################################################################
173 # Value cutoffs for cell values and ribbon formatting.
174 #
175 # You can toggle the visibility of ribbons for cells outside
176 # a min/max range. You can define one or more of these cutoffs.
177 # The cutoffs are applied to unscaled cell values.
178
179 #cell_min_value = 10
180 #cell_min_percentile = 10
181 #cell_max_value = 100
182 #cell_max_percentile = 100
183
184 # For cell values that do not pass the min/max filters above,
185 # you can specify whether they are hidden or removed. If the
186 # parameter is not defined, "hide" will be assumed.
187 # hide - cell values won't be shown, but row/col will not be resized
188 # remove - entirely remove these cells from the data set (equivalent to setting cells to missing value)
189
190 cutoff_cell_handling = hide
191
192 # The color of ribbons is by default the color of the row segment from
193 # which they originate. The block below allows you to remap the color
194 # of the ribbons based on cell percentile values. There are two ways
195 # to remap colors
196 #
197 # - color_remap=yes, color_autoremap=no
198 # Uses <percentile> blocks to define the percentile values and associated
199 # color/stroke_color characteristics for ribbons. Percentile value defined
200 # in the block (e.g. <percentile 55>) is the max percentile value for
201 # cells associated with this block.
202 # - color_remap=yes, color_autoremap=yes
203 # Uses colors associated with each percentile window of size
204 # percentile_sampling for each cell
205
206 <linkcolor>
207 color_source = row
208 percentile_source = larger
209 color_transparency = 1
210 color_remap = yes
211 color_autoremap = no
212
213 <percentile 50>
214 color = dgrey
215 transparency = 5
216 </percentile>
217
218 <percentile 60>
219 color = dgrey
220 transparency = 5
221 </percentile>
222
223 <percentile 70>
224 transparency = 1
225 </percentile>
226
227 <percentile 80>
228 transparency = 1
229 </percentile>
230
231 <percentile 90>
232 transparency = 1
233 stroke_color = black
234 stroke_thickness = 1p
235 </percentile>
236
237 <percentile 100>
238 transparency = 1
239 stroke_color = black
240 stroke_thickness = 3p
241 </percentile>
242
243 </linkcolor>
244
245 <linkparam>
246 color = vdgrey
247 #stroke_color = black
248 #stroke_thickness = 1p
249 </linkparam>
250
251 # If you are using color_autoremap=yes above, then
252 # define the percentile sampling window and
253 # the start/end HSV color values. Percentile window
254 # colors are interpolated between this HSV pair.
255 #
256 # HSV = (hue saturation value)
257 # hue=(0..360) saturation=(0..1) value=(0..1)
258
259 percentile_sampling = 5
260
261 # count - percentile based on counts
262 # value - percentile based on value
263
264 percentile_method = count
265
266 # use all values or only unique values when
267 # calculating percentiles
268 percentile_unique_only = yes
269
270 # use a function, f(X), to remap cell values when calculating percentiles
271 # for the purpose of color mapping. This allows you to apply a remapping to how
272 # colors are calculated, without actually changing the values. The remap
273 # applies only if percentile_method=value
274
275 # percentile_remap = sqrt(X)
276
277 # Which cell value set to use for percentile color mapping
278 # raw - original values
279 # filtered - values that pass min/max filters
280 # scaled - filtered values that have been scaled if use_scaling is set
281 percentile_data_domain = raw
282
283 <colors>
284 h0 = 0
285 s0 = 1
286 v0 = 1
287 h1 = 300
288 s1 = 1
289 v1 = 1
290 </colors>
291
292 # You can control the color and stroke of ribbons for each
293 # quartile (q1, q2, q3, q4). Any values defined here will
294 # overwrite colors determined by remapping.
295 #
296 # For example, if you have a lot of cells and wish to attenuate
297 # the visibility of ribbons associated with small values, you can
298 # set cell_q1_color=vvlgrey,cell_q1_nostroke=yes to fade the
299 # ribbons into the background.
300
301 #cell_q1_color = vvlgrey
302 #cell_q2_color = vlgrey
303 #cell_q3_color = lgrey
304 #cell_q4_color = red
305 #cell_q1_nostroke = yes
306 #cell_q2_nostroke = yes
307 #cell_q3_nostroke = yes
308 #cell_q4_nostroke = yes
309
310 # cell value multiplier, required when all data is small (e.g. <1), in which
311 # case set the multiplier to something like 1000 because Circos
312 # works only with integer scales
313
314 data_mult = 1
315
316 ################################################################
317 # Segment labels can be optionally set to a size that is
318 # proportional to the size of the segment. Set min/max size
319 # values here. If this line is commented out, then the label
320 # size is determined by the circos.conf file used to draw the image
321
322 #segment_label_size_range = 60,60
323
324 # progression controls how fast the label size changes from
325 # min to max (larger value of progression means values close to max
326 # are achieved for smaller segments)
327
328 segment_label_size_progression = 4
329
330 segment_label_uppercase = no
331
332 ################################################################
333 # Segment colors can be specified in the data file (in this
334 # case use row_color_col and col_color_row), otherwise colors
335 # are interpolated within an HSV range. Color interpolation can be
336 # done in two ways: based on segment index (interpolation steps through
337 # colors uniformly for each segment) and total size (interpolation
338 # steps through colors in proportion to segment size).
339
340 <segment_colors>
341 interpolate_type = size # size or count
342 h0 = 0
343 s0 = 0.8
344 v0 = 0.9
345 h1 = 300
346 s1 = 0.8
347 v1 = 0.9
348 </segment_colors>
349
350 ################################################################
351 # Shorten the labels of segments. Specify whether to do this
352 # with shorten_text=yes|no parameter and provide regular
353 # expressions in string_replace which define the text to
354 # replace.
355
356 shorten_text = yes
357
358 <string_replace>
359 IGH =
360 </string_replace>
361
362 # exit on any error
363 strict_sanity = yes
364
365 ################################################################
366 # if the segment_prefix is set, then rows and columns will be
367 # renamed to internal fields segment_prefix + DIGIT
368
369 #segment_prefix = id
370 color_prefix = color
371
372 ################################################################
373 # Delimiters
374
375 # field delimiter regular expression
376 # if this is not defined, any whitespace will be considered a delimiter
377 field_delim = \s
378
379 # collapse adjacent delimiters?
380 field_delim_collapse = yes
381
382 # remove any leading space in the input file
383 # by default, this is on - if you set this to "no", make sure that you don't have any leading spaces in your table!
384 strip_leading_space = yes
385
386 # remove quotes and thousand separators - concatenate characters to remove
387 #
388 # e.g. to remove characters a b c set remove_cell_rx=abc
389 # e.g. to remove characters " ' , set remove_cell_rx="',
390 remove_cell_rx = "',
391