ColorPhylo: A Color Code to Accurately Display Taxonomic Classifications

Abstract

Color may be very useful to visualise complex data. As far as taxonomy is concerned, color may help observing various species’ characteristics in correlation with classification. However, choosing the number of subclasses to display is often a complex task: on the one hand, assigning a limited number of colors to taxa of interest hides the structure imbedded in the subtrees of the taxonomy; on the other hand, differentiating a high number of taxa by giving them specific colors, without considering the underlying taxonomy, may lead to unreadable results since relationships between displayed taxa would not be supported by the color code. In the present paper, an automatic color coding scheme is proposed to visualise the levels of taxonomic relationships displayed as overlay on any kind of data plot. To achieve this goal, a dimensionality reduction method allows displaying taxonomic “distances” onto a Euclidean two-dimensional space. The resulting map is projected onto a 2D color space (the Hue, Saturation, Brightness colorimetric space with brightness set to 1). Proximity in the taxonomic classification corresponds to proximity on the map and is therefore materialised by color proximity. As a result, each species is related to a color code showing its position in the taxonomic tree. The so called ColorPhylo displays taxonomic relationships intuitively and can be combined with any biological result. A Matlab version of ColorPhylo is available at http://sy.lespi.free.fr/ColorPhylo-homepage.html. Meanwhile, an ad-hoc distance in case of taxonomy with unknown edge lengths is proposed.

The Cultural Evolution of Structured Languages in an Open‐Ended, Continuous World

“…To determine a color for each word, we computed the pairwise Levenshtein edit‐distances between the seven words in this particular language and derived a two‐dimensional MDS solution centered on the origin. The Cartesian coordinates in this MDS space were converted to polar coordinates and then mapped into HSV (hue, saturation, intensity value) colorimetric space: The angular coordinate was mapped to hue and the radial coordinate (scaled in [.5, 1] to avoid overly dark colors) was mapped to saturation; the intensity value was held constant at 1 (see Lespinats & Fertil, , for a full description of this method). The seven words are given in the legend alongside their assigned colors.…”

BioNames: linking taxonomy, texts, and trees

“…This makes it easier to recognise clusters of sequences from the same taxon (e.g., conspecific samples), as well as highlight possible errors (e.g., mislabelled or misidentified sequences). At present the colours are arbitrarily chosen, other schemes could be added in future (Lespinats & Fertil, 2011). …”

Phylogeny and Sequence Space: A Combined Approach to Analyze the Evolutionary Trajectories of Homologous Proteins. The Case Study of Aminodeoxychorismate Synthase

“…The phylogenetic trees (in Newick format, Lemey et al 2009) phylogenetic tree-based color-code is also provided using ColorPhylo (Lespinats and Fertil 2011). A unique color is associated to each species according to its position in the phylogenetic tree.…”