insert_drive_file.csvinsert_drive_file.nwk

Drop to add to Microreact

Creating projects

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.

Define

Two data files can be uploaded to create a Microreact:

  1. A data file in comma-separated value (csv) or tab-separated value (tsv) format, containing your data and properties for your Microreact (required).
  2. A tree file in Newick (nwk) format, specifying your tree (optional).

Data file

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.

Required column

Your data file (csv or tsv) file must must contain the following column:

idAn identifier for your data row.

The IDs in your data file must be unique and exclude full stops and commas.

Optional columns

In addition, your data file (csv or tsv) can contain the following columns:

latitudeDecimal latitude (WGS84).
longitudeDecimal longitude (WGS84).
yearParsed as number (i.e., 2016 and 16 are not the same year).
monthParsed as number (i.e, 03 and 3 are both parsed as March).
dayParsed as number.
ColumnName__colourAssign a specific colour to a data attribute.
ColumnName__shapeAssign 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__colour (or 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__autocolour(or Country__autocolor) to assign random colours to unique values of the column Country.

Example - Defining shape

If you had a column named Country you would add a column called Country__shape.

Shapes are defined using one of the following values:

circle
square
star
triangle

Example csv file

For an example dataset of mammalian species, we will define a latitude andlongitude 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.

idlatitudelongitudeCountryCountry__colourCountry__shapePedalism
Bovine46.2276382.213749FranceRedsquareFour
Gibbon15.870032100.992541ThailandGreencircleTwo
Orangutan-0.589724101.3431058SumatraBluecircleTwo
Gorilla1.37333332.290275Uganda#CC33FFcircleTwo
Chimp-0.22802115.827659CongoOrangecircleTwo
Human55.378051-3.435973UK#CCFF33circleTwo
Mouse40.463667-3.74922Spain#00FFFFsquareFour

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:

(Bovine:0.69395,(Gibbon:0.36079,(Orangutan:0.33636,(Gorilla:0.17147,(Chimp:0.19268,Human:0.11927):0.08386):0.06124):0.15057):0.54939,Mouse:1.21460);

When visualised, it renders the following tree:

You can view the demo project here.

Or download the files and create it yourself: Download CSV Download NWK

Editing projects

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.

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