Cicos plotting time

[許博程]

Hello,

I am trying to plot some histogram plot with a genome around 1 Gbp and 24 chromosomes,  but I think it is strange to plot several ticks and it takes hours to progress, I cannot imagine what will happen If I add several histograms to it. How can I adjust my configuration? Thanks~

I cannot configure successfully in my environment, so I use docker instead.

this is my command:

nohup docker run --rm -v $(pwd):/data alexcoppe/circos -conf /data/circos.conf -outputdir /data > circos.log 2>&1 &

It seems to take hours (I am not sure cuz I did not exactly see it finish) to plot one plot, I just want to test what the instruction of setting ticks on the Web site.

 

And below is my configure:

# 1.1 MINIMUM CIRCOS CONFIGURATION

#

# This is a 'hello world' Circos tutorial.

#

# Only required configuration elements are included.

#

# Subsequent tutorials in this section build on this example to

# generate a representative image with common elements found in Circos

# figures in the literature.

# Chromosome name, size and color definition

karyotype = data/karyotype.beltfish.txt

# The <ideogram> block defines the position, size, labels and other

# properties of the segments on which data are drawn. These segments

# are usually chromosomes, but can be any integer axis.

<ideogram>

<spacing>

# Spacing between ideograms. Suffix "r" denotes a relative value. It

# is relative to circle circumference (e.g. space is 0.5% of

# circumference).

default = 0.005r

# You can increase the spacing between specific ideograms.

#<pairwise hsY;hs1>

#spacing = 20r

#</pairwise>

</spacing>

# Ideogram position, thickness and fill.

#

# Radial position within the image of the ideograms. This value is

# usually relative ("r" suffix).

radius = 0.90r

# Thickness of ideograms, which can be absolute (e.g. pixels, "p"

# suffix) or relative ("r" suffix). When relative, it is a fraction of

# image radius.

thickness = 20p

# Ideograms can be drawn as filled, outlined, or both. When filled,

# the color will be taken from the last field in the karyotype file,

# or set by chromosomes_colors. Color names are discussed in

#

# https://www.circos.ca/documentation/tutorials/configuration/configuration_files

#

# When stroke_thickness=0p or if the parameter is missing, the ideogram is

# has no outline and the value of stroke_color is not used.

fill = yes

stroke_color = dgrey

stroke_thickness = 2p

</ideogram>

################################################################

# The remaining content is standard and required. It is imported from

# default files in the Circos distribution.

#

# These should be present in every Circos configuration file and

# overridden as required. To see the content of these files,

# look in etc/ in the Circos distribution.

#

# It's best to include these files using relative paths. This way, the

# files if not found under your current directory will be drawn from

# the Circos distribution.

#

# As always, centralize all your inputs as much as possible.

<image>

# Included from Circos distribution.

<<include etc/image.conf>>

</image>

# RGB/HSV color definitions, color lists, location of fonts, fill

# patterns. Included from Circos distribution.

#

# In older versions of Circos, colors, fonts and patterns were

# included individually. Now, this is done from a central file. Make

# sure that you're not importing these values twice by having

#

# *** DO NOT DO THIS ***

# <colors>

# <<include etc/colors.conf>>

# <colors>

# **********************

<<include etc/colors_fonts_patterns.conf>>

# Debugging, I/O an dother system parameters

# Included from Circos distribution.

<<include etc/housekeeping.conf>>

show_ticks = yes

show_tick_labels = yes

<ticks>

chromosome_display_default = yes

radius = dims(ideogram,radius_outer)

label_offset = 5p

orientation = out

multiplier = 1e-6

color = black

<tick>

spacing = 10u

size = 12p

thickness = 2p

color = black

show_label = yes

format = %d

</tick>

</ticks>

[Martin Krzywinski]

You're probably drawing millions of data points. Circos was not designed for this scale — it does not downsample the data.

You're probably wanting to generate a rolling average of your data and then plot that or bin frequencies across a window.

The human eye can't distinguish more than roughly 1500 positions along a circle (at typical viewing distance for a published figure) anyway, so more detail is actually not helpful and creates what might be perceived as noise.

Martin Krzywinski

science + art

https://mk.bcgsc.ca

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