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Points of View

‘Points of View’ is monthly column published by Nature Methods that deals with the fundamental aspects of visual presentation applicable to anyone who works with visual representation of data. Each month since August 2010, my co-authors and I have focused on a particular aspect of data presentation or visualization and provide easy-to-apply tips on how to create effective presentations. This series ended with the August 2013 column but the “Points of” brand lives on; Martin Krzywinski and Erica Savig are the lead authors of “Points of Significance” on statistics.

Below are links and excerpts from past columns in reverse chronological order. At the Methagora, a blog from Nature Methods, the set of 35 columns are organized into categories and was made freely available for the month of August 2013 to commemorate the completion of the series. We are working with the journal to provide the columns for free.


Nat Methods Aug. 2013

Storytelling
Relate your data to the world around them using the age-old custom of telling a story.
by Martin Krzywinski & Alberto Cairo

August 2013

A recent column made the analogy between creating figures and writing. These are similar processes that benefit equally from clarity, precision and restraint. Just as writing is made more compelling by a strong narrative, this principle also applies to the accompanying figures.


Nat Methods July 2013

Multidimensional data
Visually organize complex data by mapping them onto familiar representations of biological systems.
by Martin Krzywinski & Erica Savig

July 2013

The biological researcher can access many methods to rapidly interrogate molecular structures and mechanisms. Such experiments typically involve numerous independent variables, such as substrates, measurement modalities and experimental conditions. Many of these variables may be causally correlated, and the data likely address multiple hypotheses. This multidimensional complexity can make it difficult to design a figure that clearly presents both the structure and value of data in a manner relevant to the inquiry.


Nat. Methods June 2013

Plotting symbols
Choose distinct symbols that overlap without ambiguity and communicate relationships in data.
by Martin Krzywinski & Bang Wong

June 2013

Scatter plots require us to visually assemble data point symbols into patterns so that we can understand the relationship between the variables. Symbols can therefore have a large impact on figure legibility and clarity. Well-chosen symbols mitigate the effects of data occlusion and maintain the visual independence of different data categories.


Nat Methods May 2013

Elements of visual style
Translate the principles of effective writing to the process of figure design.
by Martin Krzywinski

May 2013

We all use words to communicate information—our ability to do so is extremely sophisticated. We have large vocabularies, understand a variety of written styles and effortlessly parse errors in real time. But when we need to present complex information visually, we may find ourselves ‘at a loss for words’, graphically speaking.


Nat Methods April 2013

Labels and callouts
Figure labels require the same consistency and alignment in their layout as text.
by Martin Krzywinski

April 2013

Last month we showed how thickness and tone can be used to make axes, ticks and grids more effective by keeping them distinct from data. The principle of visual separability applies equally to labels, as do two strategies that are frequently overlooked: consistency and alignment. These are especially relevant for labels that are attached to the figure by a connecting line (callouts).


Nat Methods Mar. 2013

Make navigational elements distinct and unobtrusive to maintain visual priority of data.
Axes, ticks and grids
by Martin Krzywinski

March 2013

Figures that present large amounts of quantitative information can be more accurately assessed when complemented with effective axes, ticks and grids. These navigational elements provide scale and aid in accurate assessment of lengths and proportions.

(POV was on hiatus in January and February).


Visualizing biological data
Data visualization is increasingly important, but it requires clear objectives and improved implementation.
by Bang Wong

December 2012

Researchers today have access to an unprecedented amount of data. The challenge is to benefit from this abundance without being overwhelmed. Data visualization for efficient exploration and effective communication is integral to scientific progress. For visualization to continue to be an important tool for discovery, its practitioners need to be present as members of research teams.


Pencil and paper
A unique set of tools facilitate thinking and hypothesis generation.
by Bang Wong & Rikke Schmidt Kjærgaard

November 2012

Creating pictures is integral to scientific thinking. In the visualization process, putting pencil to paper is an essential act of inward reflection and outward expression. It is a constructive activity that makes our thinking specific and explicit. Compared to other constructive approaches such as writing or verbal explanations, visual representation places distinct demands on our reasoning skills by forcing us to contextualize our understanding spatially.


Power of the plane
Two-dimensional visualizations of multivariate data are most effective when combined.
by Nils Gehlenborg & Bang Wong

October 2012

High-dimensional data pose a significant analytical and representational challenge. One instinctual response has been to represent data in three-dimensional (3D) space in order to capture additional information1. Given the common medium utilized for science communication, great utility can be achieved by pushing the communicative power of the endless 2D planes that surround us in the form of pieces of paper, computer monitors and video projections.


Nat. Methods Sept. 2012

Into the third dimension
Three-dimensional visualizations are effective for spatial data but rarely for other data types.
by Nils Gehlenborg & Bang Wong

September 2012

When working with high-dimensional data, it may be tempting to choose a three-dimensional (3D) spatial visualization over a two-dimensional (2D) ‘flat’ representation because it allows us an additional data dimension. However, because quantitative, categorical and relational data are often not representing spatial relationships, plotting them in 3D space adds a level of visual complexity that often makes the data more difficult to understand. It therefore can be more effective to plot these data on a 2D plane and rely on nonspatial graphical encodings to represent additional dimensions.


Nat. Methods Aug. 2012

Mapping quantitative data to color
Data structure informs choice of color maps.
by Nils Gehlenborg & Bang Wong

August 2012

Data can be classified in many ways. One useful method of classifying data for visualization is to distinguish between those with and without an inherent order. For example, a set of species (such as Escherichia coli, Drosophila melanogaster and Homo sapiens) has no intuitive ordering and is considered ‘categorical data’, whereas a list of gene expression values is ‘ordered data’ because we can sort them from lowest to highest. In a previous column, we described methods for color-coding categorical data (August 2010). Here we focus on creating color maps for quantitative data.


Nat. Methods July 2012

Representing genomic structural variation
Techniques for displaying relations between distant genomic positions.
by Cydney Nielsen & Bang Wong

July 2012

With a rapidly growing collection of genomes coming from such initiatives as the 1000 Genomes Project, the days of a single reference genome are numbered. Although the genomic sequence between any two human individuals differs only by about 0.1%, there are abundant structural and copy-number variations of different types and sizes. Effective visualization of these genomic variations is required to gain insight into the genetic basis of human health and disease. However, variation data pose new challenges to traditional genome visualization tools, which depend on linear layouts and have difficulty depicting large structural rearrangements.


Nat. Methods June 2012

Managing deep data in genome browsers
Techniques are at hand for taming the ever-growing number of data tracks.
by Cydney Nielsen & Bang Wong

June 2012

Obtaining genome-scale data has never been easier. In addition to sequencing genomes, biologists now routinely profile epigenomes, transcriptomes and proteomes. There are exciting opportunities to better understand genome regulation by integrating diverse data types into unified views. Visualization facilitates data interpretation, but designing meaningful visual depictions of these data is a challenge.


Nat. Methods May 2012

Representing the genome
The choice of visual representation of the linear genome is guided by the question being asked.
by Cydney Nielsen & Bang Wong

May 2012

Many genomics techniques produce measurements that have both a value and a position on a reference genome. The genome coordinate provides a natural ordering to these data values and is the organizing principle driving how we commonly display and navigate genomic data today. A popular plotting approach is to arrange the linear genome coordinate along the x axis and express the data value range on the y axis. This conventional representation is limiting. By using other organizational frameworks we can better extract the information of interest and make sense of its patterns.


Nat. Methods Apr. 2012

Integrating data
Different analytical tasks require different visual representations.
by Nils Gehlenborg & Bang Wong

April 2012

Different data types have their own inherent structure that makes specific visualization techniques most fitting. For example, a matrix of gene expression values for given cell measurements can be highly informative when displayed as a heat map or parallel coordinate plot. The challenge is finding visualizations that will effectively combine data types. Many research studies depend on integrating data to comprehend underlying processes. Here we explore ways to merge data that are best represented as heat maps and node-link diagrams: two common but disparate graphing techniques.


Nat. Methods Mar. 2012

Heat maps
Heat maps are useful for visualizing multivariate data but must be applied properly.
by Nils Gehlenborg & Bang Wong

March 2012

Heat maps represent two-dimensional tables of numbers as shades of colors. This is a popular plotting technique in biology, used to depict gene expression and other multivariate data. The dense and intuitive display makes heat maps well-suited for presentation of high-throughput data. Hundreds of rows and columns can be displayed on a screen. Heat maps rely fundamentally on color encoding and on meaningful reordering of the rows and columns. When either of these components is compromised, the utility of the visualization suffers.

(February 26, 2012 – #1 Most Downloaded at Nature Methods).


Nat. Methods Feb. 2012

Networks
We describe graphing techniques to support exploration of networks.
by Nils Gehlenborg & Bang Wong

February 2012

Most biological phenomena arise from the complex interactions between the cell’s many constituents such as proteins, DNA, RNA and small molecules. The graphical representations of networks can be useful in exploring this complex web of interactions. Choosing a suitable network visualization based on the patterns one hopes to highlight can yield meaningful insights into data.


Nature Methods Jan. 2012

Data exploration
Enhancement of pattern discovery through graphical representation of data.
by Noam Shoresh & Bang Wong

January 2012

Data visualization can serve two distinct purposes: to communicate research findings and to guide the data-exploration process as the scientific story is unfolding. Each goal entails a different approach to data representation, but sound graphic design principles are important in both. This column is the first in a series that will focus on data-visualization techniques intended to support data exploration.


Nat. Methods Dec. 2011

The design process
Use good design to balance self-expression with the need to satisfy an audience in a logical manner
by Bang Wong

December 2011

The primary tenets of design are utility and function. Just as objects are intuitive to use when they are well-designed, thoughtfully conceived scientific figures, slides and posters can be easy to interpret and understand. Whereas industrial design focuses on things people use, graphic design is concerned with designs people read. The design process helps us develop a visual literacy to construct presentations that are appealing and convincing.


Nat. Methods Nov. 2011

Salience and Relevance
Ensure that viewers notice the right content by making relevant information most noticeable
by Bang Wong

November 2011

In science communication, it is critical that visual information be interpreted efficiently and correctly. The discordance between components of an image that are most noticeable and those that are most relevant or important can compromise the effectiveness of a presentation. This discrepancy can cause viewers to mistakenly pay attention to regions of the image that are not relevant. Ultimately, the misdirected attention can negatively impact comprehension.


Nat. Methods Oct. 2011

Layout
Proper layout reveals the hierarchical relationship of informational elements
by Bang Wong

October 2011

Layout is the act of arranging text and images on the page according to an overall aesthetic scheme and for the purpose of clarifying a presentation. In graphic arts, it is the elephant in the room; layout underlies everything we do when we communicate visually. Well-structured content can guide readers through complex information, but when the material we present lacks order, it can confuse or, worse yet, agitate readers trying to make sense of the material.


Nat. Methods Sept 2011

Arrows
Use well-proportioned arrows sparingly and consistently as a guide through complex information
by Bang Wong

September 2011

Arrows are one of the most commonly used graphical devices in scientific figures. In the July 2011 issue of Nature Methods alone I counted nearly 300 instances of arrows; more than half of the figures contain them. Given the widespread use of arrows, it is worthwhile to take a closer look at this privileged class of diagrammatic form and how we might benefit from its use.


Nat. Methods Aug 2011

Simplify to clarify
Simplify your presentation to improve clarity
by Bang Wong

August 2011

In the past two columns I have focused on making information accessible. I discussed ways to avoid color and shift color hues to make them discernible by individuals with color vision deficiencies. In this column I focus on ways to make information apparent by simplifying its presentation.

(August 30, 2011 – #2 Most Emailed content at Nature Methods).


Nat. Methods July 2011

Avoiding Color
Choose colors appropriately to avoid bias and unwanted artifacts in visuals
by Bang Wong

July 2011

Last month I wrote about color blindness and ways to make information accessible to individuals with color vision deficiencies. I would like to continue by considering graphical alternatives to color that could improve the overall clarity and utility of data displays.


Nat. Methods Jun 2011

Color blindness
Make your graphics accessible to those with color vision deficiencies
by Bang Wong

June 2011

Since my first column on color coding1 appeared, we have received a number of e-mails asking us to highlight the issue of color blindness. One of those correspondences was published in the October 2010 issue. Here I offer guidelines to make graphics accessible to those with color vision deficiencies.


Nat. Methods May 2011

The overview figure
An economic overview figure to convey general concepts helps readers understand a research study
by Bang Wong

May 2011

Our goal when writing research papers is to convey information as clearly as possible. In past columns I have suggested several graphic design techniques to improve the clarity of figures. In addition to refining data figures, including overview figures in a research paper provides a framework for readers to understand the experimental design and reported findings.


Nat. Methods Apr 2011

Typography
Choose typefaces, sizes and spacing to clarify the structure and meaning of the text
by Bang Wong

April 2011

Typography is the art and technique of arranging type. Like a person’s speaking style and skill, the quality of our treatment of letters on a page can influence how people respond to our message. It is an essential act of encoding and interpretation, linking what we say to what people see.


Nature Methods Mar. 2011

Nat. Methods Mar. 2011

Points of review (part 2)
Examples of figure redesigns
by Bang Wong

March 2011

I will continue to demonstrate how judicious choice of graphical representations can improve visual communication. Here I will focus on data figures. ¶ The power and primary purpose of graphs is to reveal connections in data. As opposed to tables, in which there is little visual association between individual values, graphs and charts depend on readers to form patterns. In reading graphs, we observe individual data points, keep each of them in memory and construct an image from the constituents. The entire process can be exceedingly fast and attest to the power of visual perception. Graphical encoding needs to support the detection and assembly process of reading graphs.


Nat. Methods Feb 2011

Points of review (part 1)
Examples of figure redesigns
by Bang Wong

February 2011

My goal over the next two months is to show concretely how scientific figures can benefit from design principles. I will review concepts from past columns by applying them to several published figures. ¶ In the design of common objects, such as a door, when a handle is used many people will mistakenly pull even if the door is to be opened by pushing. When the handle is replaced with a flat plate, which affords pushing, people will know to push. When dealing with figures, we depend on visual cues. We want our figure’s layout to express its underlying meaning.


Nat. Methods Jan 2011

Negative space
Whitespace is a powerful way of improving visual appeal and emphasizing content
by Bang Wong

January 2011

Negative space, also known as whitespace, refers to the unmarked areas of the page. Collectively, it is the margins and the gaps between text blocks and images. Whitespace is as much a part of a composition as the titles, words and pictures. The Swiss typographer Jan Tschichold calls whitespace ‘the lungs of a good design’. In addition to giving elements breathing room, judicious use of whitespace can dramatically improve the visual appeal and effectiveness of figures, posters and slides.


Nat. Methods Dec 2010

Gestalt Principles (Part 2)
Exploit perceptual phenomena to meaningfully arrange elements on the page
by Bang Wong

December 2010

Our visual system attempts to structure what we see into patterns to make sense of information. The Gestalt principles describe different ways we organize visual data. Last month, we looked at four principles that incline us to group objects when they are made to look alike, are placed near one another, are connected by lines or are enclosed in a common space (1). This month, we will examine the principles of visual completion and continuity. These principles are useful in page layout work and when we compose figures and slides.


Nat. Methods Nov 2010

Gestalt Principles (Part 1)
Exploit perceptual phenomena to meaningfully arrange elements on the page
by Bang Wong

November 2010

Gestalt principles of perception are theories proposed by German psychologists in the 1920s to explain how people organize visual information. Gestalt is a German word meaning shape or form. The principles describe the various ways we tend to visually assemble individual objects into groups or ‘unified wholes’. They are highly relevant to the design of charts and graphs as well as the reports that contain them.


Nat. Methods Oct. 2011

Salience
Use salience to differentiate graphical symbols and speed up figure reading
by Bang Wong

October 2010

In last month’s column we explored ways to encode data that enhance ‘accuracy’ when readers decode information from graphs. This month, we will focus on salience as a way to differentiate graphical symbols and improve ‘speed’ when reading graphs.


Nat. Methods Sept. 2011

Design of Data Figures
Improve figure decoding by using strong visual cues to encode data
by Bang Wong

September 2010

Data figures or graphs are essential to life-science communication. Using these tools authors encode information that readers later decode. It is imperative that graphs are interpreted correctly. Despite the importance and widespread use of graphs, we primarily rely on our intuition, common sense and precedent in published material when creating them—a largely unscientific approach.


Nat. Methods Aug 2010

Color coding
Choose colors appropriately to avoid bias and unwanted artifacts in visuals
by Bang Wong

August 2010

Color can add dimensionality and richness to scientific communications. In figures, color is typically used to differentiate information into classes. The challenge is picking colors that are discriminable. A systematic approach to choosing colors can help us find a lineup effective for color coding.

(October 7, 2010 — #1 Most Downloaded and #4 Most Emailed at Nature Methods)