Microreact allows you to upload, visualise and explore any combination of clustering (trees), geographic (map) and temporal (timeline) data. Other metadata variables are displayed in a table. You can specify colours and/or shapes to display on the map, tree and/or timeline. A permanent URL is produced for you to share your Microreact.
Two data files can be uploaded to create a Microreact:
- A data file in comma-separated value (csv) or tab-separated value (tsv) format, containing your data and properties for your Microreact (required).
- A tree file in Newick (nwk) format, specifying your tree (optional).
This contains multiple columns/rows of data, with data variables as columns and entries as rows. There is no upper limit to the number of data variables (columns) or entries (rows) that you can define.
Your data file (
tsv) file must must contain the following column:
|An identifier for your data row.|
The IDs in your data file must be unique and exclude full stops and commas.
In addition, your data file (
tsv) can contain the following columns:
|Decimal latitude (WGS84).|
|Decimal longitude (WGS84).|
|Parsed as number (i.e., 2016 and 16 are not the same year).|
|Parsed as number (i.e, 03 and 3 are both parsed as March).|
|Parsed as number.|
|Assign a specific colour to a data attribute.|
|Assign a specific shape to a data attribute.|
If you need to geocode data you can use the following tool: www.spatialepidemiology.net/user_maps
Data without colour/shape definitions are displayed as text only on the tree leaves and within a table.
Example - Defining colour
If you had a column named
Countryyou would add a column called
Country__color) containing colour values. Colours are defined using standard HEX colour codes or valid HTML5 colour names. A colour wheel allowing you to pick colours can be found here: http://www.colorpicker.com/.
Alternatively, the column
Country can be renamed to
Country__autocolor) to assign random colours to unique values of the column
Example - Defining shape
If you had a column named
Country you would add a column called
Shapes are defined using one of the following values:
Example csv file
For an example dataset of mammalian species, we will define a
longitude for each species, along with a couple of other metadata columns: country of sample and pedalism (whether two or four legged). We will also define a
__colour and a
__shape for each different country.
Newick format tree (nwk) file
Newick notation is a way of representing bifurcating relationships between data as a tree with edge lengths using parentheses and commas. Tree leaves (tips) are represented by their names. Many programs utilize Newick as an output format and further information can be found here: en.wikipedia.org/wiki/Newick_format
If a tree file is also uploaded, Microreact links the leaf names on the nwk file to the identifiers on the id column of the csv file. Thus, the identifiers MUST be exactly the same on both the csv and the nwk files.
Example nwk string
The following Newick string describes the phylogenetic relationships between a group of well known mammalian species:
When visualised, it renders the following tree:
You can view the demo project here.
Microreact enables users to change projects and manage access through user accounts. The management interface is available by clicking on the hamburger icon at the top left of the Microreact homepage, or on the Microreact logo at the top left of a project’s webpage.
Users can log in using their Google, Twitter or Facebook accounts, and a list of all the projects created while logged in will be available to manage, allowing project name/description to be amended, data files (Newick and CSV) to be updated and access control defined.
Projects can be designated as ‘private', ‘public', or ‘public and listed' (meaning that permission is given to highlight projects on the microreact.org homepage). Users can also delete projects created while logged in, and access basic project statistics such as date created, last modified, last accessed and number of visits. Furthermore, if a project is set as public and listed the user can specify a unique custom project ID (e.g. myfavouriteproject), which replaces the random project ID set by default and is appended to the end of the permanent Microreact URL (e.g. https://microreact.org/project/myfavouriteproject).
Basic Statistics about a particular Microreact are available: Date created, last modified and last accessed. ‘View count’ the number of times the Microreact has been visited.
The ‘Danger zone’ contains a dustbin icon that can be clicked to delete a Microreact – the user will be prompted for final confirmation before full delete. Changing the Project ID: If a Microreact is ‘public and listed’ the user may click the ‘change’ button at the top left and specify a custom ID which will be used in the Microreact URL as a convenient link to the project.