Evolview User Guide: Datasets: Column plots

DATASETS

COLUMN PLOTS

overview
modifiers
the !columnPlots modifier
prepare a column of data for visualisation
examples
add column plots to collapsed trees

Overview

Column plots provides a flexable way of visualising summary information of species in a phylogenetic tree, it was inspired by the figure 6 (the column plots on the right) of a recent publication in eLife:

source: Laumer, Christopher E., Andreas Hejnol, and Gonzalo Giribet. "Nuclear genomic signals of the ‘microturbellarian’roots of platyhelminth evolutionary innovation." eLife 4 (2015): e05503.

note: thanks to Desmond Ramirez of the UCSB who brought this figure to our attention.

here is our implementation in evolview:

The tree:

(A:0.1,(B:0.2,(C:0.3,D:0.4)100:0.05)100:0.1)90:0.43;

... and the dataset:

## --
!columnplots	strokewidth=2,fontbold=1,fontsize=16,textangle=-45,spacebetweencolumns=15

## a column of data starts with a 'namedcolumn',
#it defines global options for the corresponding column
namedcolumn=thermopiles,color=purple:darker
	## followed by the following fragments
	from=A,to=C
	from=D,color=white:purple,text=?,width=20,style=circle,textangle=0

## -- 2nd column
namedcolumn=habitat,width=15
	from=A,to=B,text=aquatic,textangle=-90,color=white:lightblue
	from=C,to=D,text=?,textangle=0,color=white:darkgrey

## -- 3rd column
namedcolumn=fast evolving,color=lightgreen:darker
	from=A,style=star
	from=B,to=D
	from=C,style=none,text=*,textangle=0,width=20

Supported modifiers

Due to the complexity of the plot, we adopted here a new approach for the dataset, thus many so-called universal modifiers are no longer supported except those that are related to the legend. Below are universal modifiers that are still supported by Column plots:

Key (case insensitive)	Value	Description
!Groups or !LegendText	comma separated text	Legend texts; for example 'group_a,group_b,group_c'
!LegendStyle or !Style	rect or circle or star	shapes to be plotted before the legend texts; default = rect
!LegendColors or !Colors	comma separated color codes or names	colors to be applied to the shapes specified by LegendStyle; for example 'red,green,yellow' ;note the number of colors should match the number of legend fields
!Title or !Legend	text	title of the legend; default = name of the dataset
!ShowLegends	0 or 1	0 : hide legends; 1 : show legends
!opacity	float number between 0 to 1	opacity of the dataset

the !columnPlots modifier

here we introduce a new modifier !columnPlots to allow users to control the following aspect of the plot globally:

fill and text color
default stroke color
default stroke width
font size, italic, bold and rotation angle
column width and space between columns

please note all these global options can be overriden by local settings.

A typical !columnPlots would look like the following (NOTE: this is written in one line, not multiple lines):

!columnPlots    width=10,spaceBetweenColumns=10,color=green:red,strokewidth=1,textangle=-60,style=rect,roundedcorner=5,fontsize=14

please remember always use a 'TAB' character to separate !columnPlots from its value.

The value of !columnPlots is mandatory; it can be any of the following options, individually or in combination:

key	alternative value	description
width=10	any integer >= 0	set column width, default = 10
spaceBetweenColumns=10	any integer >= 0	set space between columns, default = 10
style=rect	any of the following:none,rect,circle,star,check,triangle	style / shape to be plotted, default = rect
fontsize=10	any integer >= 0	set font size for columns labels, default = 14
fontitalic=0	1	set font italic for columns labels, default = 0
fontbold=0	1	set font bold for columns labels, default = 0
color=red, or color=red:blue	any valid html color name, e.g. green, darkblue ..., or hex html color, e.g. #FF00FF	set fill and optional stroke color; fill color will be also applied to column labels, default = black; see examples below for detail
strokewidth=1	any integer >=1	set strokewidth, valid only when the strokecolor is set, default = 1; see examples below for detail

Please note that Evolview supports the use of "darker", "brighter" and "lighter" as stroke colors. For example, the following usages are all valid:

red:darker
#FF00FF:lighter
darkblue:brighter

When 'darker' or 'brighter'/'lighter' is used, the stroke color will be 20% darker or brighter than the specified color.

See here for more details.

Prepare a column of data for visualisation

As shown in the previous example, a column of data often consists of two parts,

a line of text starts with a mandatory filed 'namedcolumn=name of the column', followed by any numbers of the options mentioned in the table above, for example:
- namedcolumn=thermopiles,color=purple:darker
- namedcolumn=habitat,width=15 the options following 'namedColumn' control the displaying styles of current column, and overrides the corresponding global options.
several lines of text, each line defines a fragment / segment to be plotted. For example:
- from=A,to=C
- from=D,color=white:purple,text=?,width=20,style=circle,textangle=0 the 'fragment' line should contain the following elements:
- the starting point, i.e. the name of the leaf node, of the fragment using 'from='; mandatory
- an optional ending point / the name of a leaf node using 'to='
- any numbers of the options mentioned in the above table; optional. These options control the displaying styles of current fragment, and overrides the corresponding global options

Here is an example:

## a column of data starts with a 'namedcolumn',
##it defines global options for the corresponding column
namedcolumn=thermopiles,color=purple:darker
	## followed by the following fragments
	from=A,to=C
	from=D,color=white:purple,text=?,width=20,style=circle,textangle=0

Note:

The dataset is case-insensitive

the indentation at the begining of the framents is optional

Examples

Example 1. a column with two fragments, one span three leaf nodes, while the other spans only one.:

## --
## -- some global options
!columnplots	strokewidth=2,fontbold=1,fontsize=16,textangle=-45

## -- a column with two fragments, note how the stroke color is defined
namedcolumn=thermopiles,color=lightblue:darker
	## note: the indentation is optional
	from=A,to=C
	from=D

Example 2. try change the style / shape of the fragments, however it only work when a fragment spans only one leaf node:

##
## -- some global options
!columnplots	strokewidth=2,fontbold=1,fontsize=16,textangle=-45

## -- a column with two fragments, note how the stroke color is defined
namedcolumn=thermopiles,color=lightblue:darker
	## try change the style / shape, but it wouldn't work here
	from=A,to=C,style=star
    ## but, it will work here
	from=D,style=star

Example 3. now try change the width of the fragments:

##
## -- some global options
!columnplots	strokewidth=2,fontbold=1,fontsize=16,textangle=-45

## -- set width to 20, it will apply to both fragments
namedcolumn=thermopiles,color=lightblue:darker,width=20
	from=A,to=C,style=star
	from=D,style=star

Example 4. of course you can change the widths of the fragments individually:

##
## -- some global options
!columnplots	strokewidth=2,fontbold=1,fontsize=16,textangle=-45

## please note, width=25 here specifies the overall plot width of current column,
##    it is thus meaningful even it is overridden later.
namedcolumn=thermopiles,color=lightblue:darker,width=25
	from=A,to=C,width=10
	from=D,style=star,width=20

Example 5. we know for sure the first three species are thermophilic, but the last one???

##
## -- some global options
!columnplots	strokewidth=2,fontbold=1,fontsize=16,textangle=-45

namedcolumn=thermopiles,color=#FF33CC:darker,width=25
	from=A,to=C,width=10
	from=D,style=circle,color=white:darkgrey,width=20,text=?,textangle=0

Example 6. now we'd like the readers to pay more attention to species A and C:

##
## -- some global options
!columnplots	strokewidth=2,fontbold=1,fontsize=16,textangle=-45

namedcolumn=thermopiles,color=lightblue:darker,width=25
	from=A,to=C,width=10

	## -- don't forget to set style=none
	from=A,style=none,text=*,fontsize=16,textangle=0
	from=C,style=none,text=*,fontsize=16,textangle=0

	from=D,style=circle,color=white:darkgrey,width=20,text=?,textangle=0

Example 7. of course we can have multiple columns in a dataset:

##
!columnplots	strokewidth=2,fontbold=1,fontsize=16,textangle=-45,spacebetweencolumns=15

## a column of data starts with a 'namedcolumn',
## it defines global options for the corresponding column
namedcolumn=thermopiles,color=purple:darker
	## followed by the following fragments
	from=A,to=C
	from=D,color=white:purple,text=?,width=20,style=circle,textangle=0

## -- 2nd column
namedcolumn=habitat,width=15
	from=A,to=B,text=aquatic,textangle=90,color=white:lightblue,fontsize=14
	from=C,to=D,text=?,textangle=0,color=white:darkgrey

## -- 3rd column
namedcolumn=fast evolving,color=lightgreen:darker
	from=A,style=star
	from=B,to=D
	from=C,style=none,text=*,textangle=0,width=20

Please NOTE:

the plot is optimized for cladogram and phylogram, thus it wouldn't be as pretty in circular mode
please send us (evolgenius.team@gmail.com) email if you have encountered any problems using EvolView, attach your tree and datasets if necessary
please also send us your suggestions and feature requests!

Add column plots to collapsed trees

Evolview supports collapsing at internal nodes; collapsed nodes are treated as leaf nodes. It is therefore very straightforward to add column plots to a collapsed tree. See here for more information.

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