visualizing quantitative information
martin krzywinski
outline
best practices of graphical data design data-to-ink ratio cartjunk circos
the visual display of quantitative information edward r tufte, 2001, 2nd ed
graphical displays essentials
show the data induce viewer to think about substance rather than methodology encourage eye to compare different pieces of data avoid distorting what the data represents present many numbers in a small space make large data sets coherent reveal data at several levels of detail broad overview and fine structure
the visual display of quantitative information edward r tufte, 2001, 2nd ed
graphics reveal data and patterns
each of these sets are described by the same linear model
anscombes quartet each of the values below is the same for each set number of points average x average y regression line standard error of slope sum of squares q residual sum of squares correlation coefficient r2
the visual display of quantitative information edward r tufte, 2001, 2nd ed
graphics organize complex information
some data sets are naturally better represented visually each of these data maps portrays ~21,000 numbers although very dense, the images draw attention to hot spots dense
death rate from various cancers females males
the visual display of quantitative information edward r tufte, 2001, 2nd ed
graphics organize dense information
locations and boundaries 3 , of 30,000 communes in France 240,000 numbers
the visual display of quantitative information edward r tufte, 2001, 2nd ed
graphics organize dense information
1,024 x 2,222 sky divisions 10 grey tones pixel grey value denotes number of galaxies in corresponding sky region density of data commensurate with a photograph, but quantitative
the visual display of quantitative information edward r tufte, 2001, 2nd ed
graphics simplify complex information
TGV
the visual display of quantitative information edward r tufte, 2001, 2nd ed
when the image is the data
the visual medium is ideal for d i ti f depicting multivariate lti i t data arguably univariate and bivariate data should be tabularized, within reason this example shows a plot for a case where data cannot be easily parametrized
the visual display of quantitative information edward r tufte, 2001, 2nd ed
parametrization of multivariate data
the 2D plane can depict high-dimension data hi h di i d t chernoff faces are data encodings designed for easy identification of outliers parameters are mapped to d head shape, eye distance, nose and lip size smoothly varying data corresponds to smoothly varying chernoff population l
the visual display of quantitative information edward r tufte, 2001, 2nd ed
data to ink data-to-ink ratio
proportion of graphics ink devoted to the non-redundant display of data information i f ti 1.0 proportion of a graphic that can be erased without loss of data information data-to-ink ratio should always be maximized, within reason
the visual display of quantitative information edward r tufte, 2001, 2nd ed
data to ink data-to-ink ratio
high shockingly low
the visual display of quantitative information edward r tufte, 2001, 2nd ed
data to ink data-to-ink ratio
original deleted components modified to increase data-to-ink ratio
the visual display of quantitative information edward r tufte, 2001, 2nd ed
shrink your graphics
dense data can be depicted within a small area without loss of clarity ll ith t l f l it as long as data-to-ink ratio is high good graphics are informative dense multivariate
strive to give your viewer the greatest number of ideas in the shortest time with the least ink ith in the smallest space
the visual display of quantitative information edward r tufte, 2001, 2nd ed
cartjunk
excessive use of grids and patterns cause perceived vibrations avoid hatched patterns to limit moire avoid excessive use of decorative forms
the visual display of quantitative information edward r tufte, 2001, 2nd ed
the shimmering statistic
natural eye tremor and dense fill dd patterns produce a shimmering effect this is annoying and tiring
the visual display of quantitative information edward r tufte, 2001, 2nd ed
circos
there are many genome browsers and yg visualizers already available do we really need another one? communicating data visually critical for large data sets yp there certain types of data that obfuscate common diagram formats
standard 2D plots (2 perpendicular axes) are inadequate
scalar mappings
scalar valued mappings are common and easily handled
input genomic position i a scalar i i t i iti is l input t when the output is real-valued (GC content, conservation, etc) use a histogram, line plot, scatter plot genome position on x-axis function value on y-axis
f :g y
genome to genome genome-to-genome mappings
output scalar is often a genome position (G2G)
range may b the same genome, or a different genome be th diff t G2G is also common, but less easily handled
f : g g
genome position genome position
drawing G2G mappings
drawing G2G mappings
Genome Res. 2003 Jan;13(1):37-45
drawing G2G mappings
Genome Res. 2003 Jan;13(1):37-45
drawing G2G mappings
Genome Res. 2005 May;15(5):629-40
drawing G2G mappings
sc7 I
sc15 I
I chr04 chr09
I ch
drawing G2G mappings
Genome Res. 2003 Jan;13(1):37-45
drawing G2G mappings
http://www.egg.isu.edu/Members/deborah/genomics
drawing G2G mappings
http://www.genome.wustl.edu/projects/human/chr7paper/chr7data/030113/segmental/index.php
drawing G2G mappings
dealing with G2G mappings
reduce information content in figures
plot/colourmap target chromosome, not position l t/ l t t h t iti
f : g g c
dealing with G2G mappings
Genome Res. 2004 Apr;14(4):685-92
reduce sampling
Genome Res. 2005 Jan;15(1):98-110
rearrange axes
partition data
recompose axis layout circos
circos
written in Perl Apache-style configuration file plain text data input p PNG output
G2G in circos
display characteristics of most elements are f t l t customizable data driven data-driven formatting rules support for data layers
2D data in circos
2D data in circos
box
scatter
line
2D data in circos
tiles tiles
histogram heatmaps
chr2
non linear non-linear scaling
global scaling scale of each id f h ideogram can be adjusted e.g. e g chr 1 drawn at 8x local scaling any region can be locally expanded or d d contracted e.g. e g 100-150 Mb on chr1 expanded 5x
non linear non-linear scaling
circos in comparative genomics
mouse chr3 mouse chr1
human chr1
circos in comparative genomics
chlamydia D fingerprint map vs chlamydia D sequence
circos in comparative genomics
chlamydia L fingerprint map vs chlamydia D sequence
blast of regions of chr14 vs chr22 alignments drawn as ribbons ibb
single alignment
circos is flexible
mkweb.bcgsc.ca/circos
download documentation tutorials circos art
