Schemaball
Circular visualization of database schemas
Schemaball was published in SysAdmin Magazine (Krzywinski, M. Schemaball: A New Spin on Database Visualization (2004) Sysadmin Magazine Vol 13 Issue 08). Who cites Schemaball?
These tutorials illustrate different features of Schemaball. Tutorials are divided into sections. Each section covers a particular aspect of a feature or set of features. Each section has its own documentation, configuration file and schema ball image.
tutorial 4
Highlighting schema diagram elements.
NAME
sbtut_04 - highlighting schema elements
SYNOPSIS
<table> <highlight_rx> misc feature </highlight_rx> fill_hi = acff96 outline_hi = ffffff </table>
<table> <highlight_rx> !_feature </highlight_rx> fill_hi = c2cdef outline_hi = ffffff </table>
<highlight_rx> ^.*feature.*__ </highlight_rx>
<highlight_rx> __.*feature.*$ </highlight_rx>
PURPOSE
This tutorial will illustrate how to use highlighting to apply a different colour scheme to elements in the schema diagram.
TUTORIAL
Highlighting is controlled in a similar manner to visibility. The element blocks <link> and <table> have a highlight_file parameter and a <highlight_rx> block, used to store regular expressions applied to the names of the elements. When an element name matches, its colour scheme will be determined by FIELD_hi elements (e.g. stroke_hi, fill_hi, etc).
Highlighting Tables
Highlighting specific tables is best done using the <highlight_rx> block. Here, tables whose names contain the strings ``misc'' or ``feature'' will be coloured differently. You can independently adjust the fill colour and the width and colour of the glyph outline.
<table> ... <highlight_rx> misc feature </highlight_rx> ... fill_hi = acff96 outline_hi = ffffff ... </table>
The resulting image is sbtut_04_01.png
Fading Tables
The highlight feature can be subverted to fade all but a given set of tables. To select all tables except those that match a regular expression, append !_ to the regular expression. This configuration will apply the highlight colours, designed to fade into the background, to all tables except those which have ``feature'' in their names.
<table> ... <highlight_rx> !_feature </highlight_rx> ... fill_hi = c2cdef outline_hi = ffffff ... </table>
The resulting image is sbtut_04_02.png
Highlighting Links
Highlighting constraint links is done the same way as tables. Remember that links are named like table1__table2. This convention allows you to create regular expressions to select links that start at a table (e.g. table1__) or end at a table (e.g. __table2).
When highlighting links, you can control the colour and thickness of the line. This configuration will highlight all links starting and ending at a table whose name contains the string ``feature''.
<link> ... <highlight_rx> feature </highlight_rx> ... color_hi = acff96 stroke_hi = 3 ... </link>
The resulting image is sbtut_04_03.png.
To highlight only links which start at a given table, or tables, use the fact that the link name is table1__table2. The following highlights only those links which start at a table with a name containing ``feature''.
<link> ... <highlight_rx> ^.*feature.*__ </highlight_rx> ... color_hi = acff96 stroke_hi = 3 ... </link>
The resulting image is sbtut_04_04.png.
Similarly, to highlight all links which lead to feature tables,
<link> ... <highlight_rx> __.*feature.*$ </highlight_rx> ... color_hi = acff96 stroke_hi = 3 ... </link>
The resulting image is sbtut_04_05.png.
By creating multiple layers with specific links highlighted in different colours you can achieve flexible compositions.
HISTORY
- v0.01 17 May 2004
Created tutorial.
BUGS
Please report errors and suggestions to martink@bcgsc.ca
AUTHOR
Martin Krzywinski, mkweb.bcgsc.ca, martink@bcgsc.ca
$Id: schemaball,v 1.5 2003/10/27 20:25:11 martink Exp $
CONTACT
Martin Krzywinski Genome Sciences Centre Vancouver BC Canada www.bcgsc.ca mkweb.bcgsc.ca martink@bcgsc.ca
configuration
################################################################ # # Schemaball configuration file # # Tutorial 04 # # sbtut_04_01.conf - highlighting schema elements # <db> sqlfile = tutorial/04/hs.sql </db> <linkrule fieldregex> fieldrx = ^(\w+)_([a-z]+)$ use = yes avoidself = yes <fields> table = 0 field = 1 </fields> </linkrule> <image> file = /home/httpd/htdocs/worldatwar/schema.png size = 1000 glyphradius = 0.7 background = c2cdef foreground = 61,95,197 <elements> <link> show_links = yes color = 3d5fc5 stroke = 2 anchor = edge type = bezier </link> <bezier> resolution = 100 radius = 0.1 </bezier> <label> font = tahoma.ttf size = 10 </label> <table> size = 25 fill = 255,219,150 stroke = 2 outline = 3d5fc5 <highlight_rx> misc feature </highlight_rx> fill_hi = acff96 outline_hi = ffffff </table> </elements> </image>
################################################################ # # Schemaball configuration file # # Tutorial 04 # # sbtut_04_02.conf - highlighting schema elements # <db> sqlfile = tutorial/04/hs.sql </db> <linkrule fieldregex> fieldrx = ^(\w+)_([a-z]+)$ use = yes avoidself = yes <fields> table = 0 field = 1 </fields> </linkrule> <image> file = /home/httpd/htdocs/worldatwar/schema.png size = 1000 glyphradius = 0.7 background = c2cdef foreground = 61,95,197 <elements> <link> show_links = yes color = 3d5fc5 stroke = 2 anchor = edge type = bezier </link> <bezier> resolution = 100 radius = 0.1 </bezier> <label> font = tahoma.ttf size = 10 </label> <table> size = 25 fill = 255,219,150 stroke = 2 outline = 3d5fc5 <highlight_rx> !_feature </highlight_rx> fill_hi = c2cdef outline_hi = 7b96e4 </table> </elements> </image>
################################################################ # # Schemaball configuration file # # Tutorial 04 # # sbtut_04_03.conf - highlighting schema elements # <db> sqlfile = tutorial/04/hs.sql </db> <linkrule fieldregex> fieldrx = ^(\w+)_([a-z]+)$ use = yes avoidself = yes <fields> table = 0 field = 1 </fields> </linkrule> <image> file = /home/httpd/htdocs/worldatwar/schema.png size = 1000 glyphradius = 0.7 background = c2cdef foreground = 61,95,197 <elements> <link> show_links = yes color = 3d5fc5 stroke = 2 anchor = edge type = bezier <highlight_rx> feature </highlight_rx> color_hi = acff96 stroke_hi = 3 </link> <bezier> resolution = 100 radius = 0.1 </bezier> <label> font = tahoma.ttf size = 10 </label> <table> size = 25 fill = 255,219,150 stroke = 2 outline = 3d5fc5 </table> </elements> </image>
################################################################ # # Schemaball configuration file # # Tutorial 04 # # sbtut_04_04.conf - highlighting schema elements # <db> sqlfile = tutorial/04/hs.sql </db> <linkrule fieldregex> fieldrx = ^(\w+)_([a-z]+)$ use = yes avoidself = yes <fields> table = 0 field = 1 </fields> </linkrule> <image> file = /home/httpd/htdocs/worldatwar/schema.png size = 1000 glyphradius = 0.7 background = c2cdef foreground = 61,95,197 <elements> <link> show_links = yes color = 3d5fc5 stroke = 2 anchor = edge type = bezier <highlight_rx> ^.*feature.*__ </highlight_rx> color_hi = acff96 stroke_hi = 3 </link> <bezier> resolution = 100 radius = 0.1 </bezier> <label> font = tahoma.ttf size = 10 </label> <table> size = 25 fill = 255,219,150 stroke = 2 outline = 3d5fc5 </table> </elements> </image>
################################################################ # # Schemaball configuration file # # Tutorial 04 # # sbtut_04_05.conf - highlighting schema elements # <db> sqlfile = tutorial/04/hs.sql </db> <linkrule fieldregex> fieldrx = ^(\w+)_([a-z]+)$ use = yes avoidself = yes <fields> table = 0 field = 1 </fields> </linkrule> <image> file = /home/httpd/htdocs/worldatwar/schema.png size = 1000 glyphradius = 0.7 background = c2cdef foreground = 61,95,197 <elements> <link> show_links = yes color = 3d5fc5 stroke = 2 anchor = edge type = bezier <highlight_rx> __.*feature.*$ </highlight_rx> color_hi = acff96 stroke_hi = 3 </link> <bezier> resolution = 100 radius = 0.1 </bezier> <label> font = tahoma.ttf size = 10 </label> <table> size = 25 fill = 255,219,150 stroke = 2 outline = 3d5fc5 </table> </elements> </image>
Nasa to send our human genome discs to the Moon
We'd like to say a ‘cosmic hello’: mathematics, culture, palaeontology, art and science, and ... human genomes.
Comparing classifier performance with baselines
All animals are equal, but some animals are more equal than others. —George Orwell
This month, we will illustrate the importance of establishing a baseline performance level.
Baselines are typically generated independently for each dataset using very simple models. Their role is to set the minimum level of acceptable performance and help with comparing relative improvements in performance of other models.
Unfortunately, baselines are often overlooked and, in the presence of a class imbalance5, must be established with care.
Megahed, F.M, Chen, Y-J., Jones-Farmer, A., Rigdon, S.E., Krzywinski, M. & Altman, N. (2024) Points of significance: Comparing classifier performance with baselines. Nat. Methods 20.
Happy 2024 π Day—
sunflowers ho!
Celebrate π Day (March 14th) and dig into the digit garden. Let's grow something.
How Analyzing Cosmic Nothing Might Explain Everything
Huge empty areas of the universe called voids could help solve the greatest mysteries in the cosmos.
My graphic accompanying How Analyzing Cosmic Nothing Might Explain Everything in the January 2024 issue of Scientific American depicts the entire Universe in a two-page spread — full of nothing.
The graphic uses the latest data from SDSS 12 and is an update to my Superclusters and Voids poster.
Michael Lemonick (editor) explains on the graphic:
“Regions of relatively empty space called cosmic voids are everywhere in the universe, and scientists believe studying their size, shape and spread across the cosmos could help them understand dark matter, dark energy and other big mysteries.
To use voids in this way, astronomers must map these regions in detail—a project that is just beginning.
Shown here are voids discovered by the Sloan Digital Sky Survey (SDSS), along with a selection of 16 previously named voids. Scientists expect voids to be evenly distributed throughout space—the lack of voids in some regions on the globe simply reflects SDSS’s sky coverage.”
voids
Sofia Contarini, Alice Pisani, Nico Hamaus, Federico Marulli Lauro Moscardini & Marco Baldi (2023) Cosmological Constraints from the BOSS DR12 Void Size Function Astrophysical Journal 953:46.
Nico Hamaus, Alice Pisani, Jin-Ah Choi, Guilhem Lavaux, Benjamin D. Wandelt & Jochen Weller (2020) Journal of Cosmology and Astroparticle Physics 2020:023.
Sloan Digital Sky Survey Data Release 12
Alan MacRobert (Sky & Telescope), Paulina Rowicka/Martin Krzywinski (revisions & Microscopium)
Hoffleit & Warren Jr. (1991) The Bright Star Catalog, 5th Revised Edition (Preliminary Version).
H0 = 67.4 km/(Mpc·s), Ωm = 0.315, Ωv = 0.685. Planck collaboration Planck 2018 results. VI. Cosmological parameters (2018).
constellation figures
stars
cosmology
Error in predictor variables
It is the mark of an educated mind to rest satisfied with the degree of precision that the nature of the subject admits and not to seek exactness where only an approximation is possible. —Aristotle
In regression, the predictors are (typically) assumed to have known values that are measured without error.
Practically, however, predictors are often measured with error. This has a profound (but predictable) effect on the estimates of relationships among variables – the so-called “error in variables” problem.
Error in measuring the predictors is often ignored. In this column, we discuss when ignoring this error is harmless and when it can lead to large bias that can leads us to miss important effects.
Altman, N. & Krzywinski, M. (2024) Points of significance: Error in predictor variables. Nat. Methods 20.
Background reading
Altman, N. & Krzywinski, M. (2015) Points of significance: Simple linear regression. Nat. Methods 12:999–1000.
Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Logistic regression. Nat. Methods 13:541–542 (2016).
Das, K., Krzywinski, M. & Altman, N. (2019) Points of significance: Quantile regression. Nat. Methods 16:451–452.