Mercurial > repos > davidvanzessen > argalaxy_tools
diff report_clonality/circos/housekeeping.conf @ 0:afe85eb6572e draft
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author | davidvanzessen |
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date | Mon, 29 Aug 2016 05:41:20 -0400 |
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children | 124b7fd92a3e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/report_clonality/circos/housekeeping.conf Mon Aug 29 05:41:20 2016 -0400 @@ -0,0 +1,230 @@ +# Housekeeping parameters, which must be included +# at the top level of the configuration. +# +# Don't adjust these, unless you know what you are doing, or +# feel like experimenting + +anglestep = 0.5 +minslicestep = 10 +beziersamples = 40 # bezier curves are drawn piece-wise + # linear, with this many samples +debug = no +warnings = no +imagemap = no +paranoid = yes + +units_ok = bupr +units_nounit = n + +# \t tab +# \s any whitespace +file_delim = \s +# collapse adjacent whitespace +# e.g. two spaces are treated as one, not as a missing field +file_delim_collapse = yes + +# Record delimiter for parameter values that are lists, such as +# hs1:0.25;hs2:0.10. By default, both ; and , are accepted +# +# e.g. hs1:0.25,hs2:0.10 +# hs1:0.25;hs2:0.10 +list_record_delim = \s*[;,]\s* +# Field delimiter specifies the assignment operator, e.g. +list_field_delim = \s*[:=]\s*] + +# Rule fields and other parameters accept var(VARIABLE) syntax +# to reference parameters of data points. By default, if +# VARIABLE does not exist, Circos quits with an error, unless +# the skip parameter below is set. +# +# This feature is useful when you have data that don't always +# have the same options. For example, +# +# chr1 10 20 a=10 +# chr1 50 60 b=10 +skip_missing_expression_vars = no + +# In old versions, data point parameters were referenced using _NAME_ +# syntax. This has been replaced with var(NAME). The _NAME_ syntax is +# deprecated (for example, it will break when dealing with fields like +# gene_a_1). If you must use it, set the parameter below. + +legacy_underline_expression_syntax = no + +# Magnification factor for text in SVG files. +svg_font_scale = 1.3 + +# default font - pick one of the keys from <fonts> block +default_font = default +# default font name is used for SVG files for cases where +# the font definition does not include a name +# see etc/fonts.conf for details +default_font_name = Arial +default_font_color = black + +# default color for cases when color is not specified +default_color = black + +<guides> +thickness = 1 +size = 5 +type = outline +<object> +all = no +ideogram = no +ideogram_label = no +</object> +<color> +default = lblue +text = red +</color> +</guides> + +# Receive debug messages about actions +# +# Comma-separated list of one or more of the following +# +# summary - top level indications of what's happening +# chrfilter - ideogram filtering (parsing 'chromosomes' parameter) +# conf - configuration file +# counter - plot counters +# spacing - ideogram spacing +# scale - ideogram scaling +# ideogram - ideogram reporting +# anglepos - report angle positions for base pair coordinates +# zoom - zoom regions +# layers - specific plot z-layers +# rules - dynamic rules +# text - text tracks +# heatmap - detailed heatmap reports +# brush - brushes +# color - color allocation and definition +# ticks - tick marks and labels +# timers - some benchmark timings +# cache - caches +# _all - turn on all groups +debug_group = summary + +# run length duration after which timing report is automatically +# generated at the end of the run +debug_auto_timer_report = 30 + +debug_word_separator = " " +debug_undef_text = _undef_ +debug_empty_text = _emptylist_ + +# parameters passed to functions can be +# validated to check consistency. turn this +# off to speed things up +debug_validate = yes + +# Reformat numbers in debug output for consistency. +# If you have a lot of debug output (e.g. -debug_group _all) +# this will slow things considerably. +debug_output_tidy = no + +# pixel sub-sampling for text tracks +text_pixel_subsampling = 1 +# array or span - use 'span' if applying snuggle refinement +text_snuggle_method = array + +# restrict names of parameters? +# if 'yes' then only certain named parameters are allowed within +# blocks and option fields for data +# +# if 'no' then you can define parameters with any name what-so-ever, +# useful if you wish to define states or labels for your data +# +# e.g. hs1 10 20 0.5 paired=yes,special=no,myvar=0.5 +# +# ordinarily, 'paired', 'special' and 'myvar' would not be allowed +restrict_parameter_names = no + +# Unless set to 'yes', parameter names will be converted to lowercase +case_sensitive_parameter_names = no + +# The location of configuration and data files will be guessed if +# (a) configuration file is not specified +# (b) data file paths are relative +# Circos will look in the following locations, where +# SCRIPTPATH is the location of the 'circos' script (e.g. /usr/local/bin) and +# CWD is the current directory (where the 'circos' command was executed). +# All paths under CWD will be scanned first, then under SCRIPTPATH. +# +# {CWD,SCRIPTPATH}/. +# {CWD,SCRIPTPATH}/.. +# {CWD,SCRIPTPATH}/etc/ +# {CWD,SCRIPTPATH}/../etc +# {CWD,SCRIPTPATH}/../../etc +# {CWD,SCRIPTPATH}/data +# {CWD,SCRIPTPATH}/../data +# {CWD,SCRIPTPATH}/../../data +# +# If you would like to prepend this list with custom directories for +# data files, enter them as a CSV list here +# data_path = /home/martink/circos-tutorials +# If the cache is static, it will always be used and will not be updated +# unless it is deleted (use -color_cache_rebuild on the command line). +# Otherwise, the cache will be updated if +# - config file is newer than cache file +# - list of colors in config file is different than in cache file +color_cache_static = yes +color_cache_file = circos.colorlist +color_lists_use = yes +# if the directory is not defined, then the system will guess a temporary +# directory compatible with your operating system (using File::Temp) +# color_cache_dir = /tmp + +# Make some functions faster. This should always be 'yes' unless you +# want things to run slowly or suspect deep issues. +memoize = yes + +# This is a debugging flag and should be set to 'no' for regular use +quit_on_dump = yes + +offsets = 0,0 + +# Maximum number of image and data elements. If these are exceeded, +# Circos will quit with an error. These values are arbitrary, but in +# my experience images with significantly more data points than this +# are uninterpretable. + +max_ticks = 5000 +max_ideograms = 200 +max_links = 25000 +max_points_per_track = 25000 + +# What to do when data is found for an ideogram that does not appear in the karyotype file. + +# Set to 'skip' or 'exit' +undefined_ideogram = skip + +# Number of iterations for determining ideogram sizes when +# relative scale is used. +relative_scale_iterations = 10 + +# min, max, average, mode - based on scale statistics of ALL ideograms +# minadj, maxadj, averageadj, modeadj - based on scale statistics of adjacent ideograms +# +# You can specify a fixed scale for spacing using a floating value +# +# e.g. relative_scale_spacing = 1.5 +relative_scale_spacing = mode + +# What to do with out-of-range data. Either 'clip' or 'hide' +data_out_of_range = clip + +# Track default directory +track_defaults = etc/tracks + +# Use round brushes for elements with thickness greater than round_brush_min_thickness? +round_brush_use = yes +round_brush_min_thickness = 5 + +# Use anti aliasing, where possible? I've seen bugs in some gd libraries +# that cause artefacts to appear when lines are anti-aliased. If your +# image contains unexpected elements, turn aa off. +anti_aliasing = yes + +# A parameter that must be set. Checks whether this file was imported. +housekeeping = yes