annotate report_clonality/circos/housekeeping.conf @ 48:efe0a2b5d163 draft

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# 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