These tools were built as needed to automate some tasks of my work or of my colleagues. As so, they are distributed in the hope that they will be useful as they were, but there is I have no intention to keep updating them regularly. If you find them useful and have some comments or questions you can contact me (ptarroso at cibio.up.pt).

ExportNet

The zipped file includes one Python script to export an fdi network to an editable pdf. To use the script you need Python installed in your system with the modules Numpy/Scipy, Matplotlib and NetworkX. To convert your networks, just run the script in the folder where you have your fdi files and it will automatically generate one editable pdf for each.

The last version (v.8) generates pie charts for each node if information about frequencies is available either in the fdi file or with two additional files (examples attached to zip file):

• lineage file (text file with ".lin" extension) with lineage code for each sample
• lineage color (text file with ".col" extension) with a color code for each lineage

The color can be the hexadecimal code extracted by any image manipulation, illustration or color scheme software (e.g. gimp, Inkscape, Adobe Kuler, etc) or using 'matplotlib' defined colors (available colors and example attached to zip file).

You may edit the script code in any text editor to define some script options:

• 'mutlabels': changes the representation of the mutation labels. 0 - mutation steps not represented; 1 - mutation steps represented by dots (default); 2- labels representing the mutational step number).
• 'draw_pie': can be set to either true or false
• 'multi': a multiplier value for the size of nodes in the generated pdf.
• 'logTrans': a logarithm transformation of the node size. Either true or false (default).
  

Windows users should download the module binaries in the above links and install them (if you already have Python installed in your system, be sure to download the module for your Python version).

Mac users may use the Scipy Superpack which installs all the components, except NetworkX (see the webpage for more details about installing on Mac) and, if you don't like the Terminal, you may use a Automator action (see here) to execute the script.

For Linux users, just install the module packages with your favorite package manager or compile them from source.

Spatial tools for ecological niche modelling

These tools have been highly requested by colleagues to simplify the process of converting rasters to ascii format, to create consensus maps from multiple prediction rasters and to calculate correlations between maps in ArcMap. It was tested with ArcGIS 10 and it will not work with previous versions.

The installation is quite simple: download the compressed file, extract the tbx file in the zip file and copy it to the folder ArcGIS inside "My Documents" folder. It will be available in the ArcCatalog and you can drag it to the toolbox.

JoinSplit plugin for QGIS

This plugin for QGIS (version >= 2.0) helps the process of joining one spatial layer to a table without geometry and than split each column to an individual shapefile. The original application for this plugin was to join species presence information in a pivot table with a polygon grid and export the presence squares for each species as distinct shapefiles.

In the plugin graphical interface the user may choose the spatial layer and table to join from the list of available layers in the table of contents. A common field MUST be shared between the spatial layer and table with the same name. The user may also select the fields from the table to export as individual files and, optionally, a style file to display the created layers. The fields to be exported MUST be numeric.

The plugin is available in a GIT repository.. To install, just copy a folder "JoinSplit" with all files to your QGIS plugin folder. This folder is usually found in "YOUR_HOME_DIR/.qgis/python/plugins" but check this site for additional details. Inside QGIS you can find the plugin listed in the plugin manager.

Table2style plugin for QGIS

Table2style is a plug-in for QGIS (version >= 2.0; http://www.qgis.org). It reads data from a table containing pixel values and a correspondent description and creates a color style and legend for a raster. If the table does not contain RGB values, random colors are attributed to each class in the description.

This plugin also exports a the classification to a new raster, where pixels with values corresponding to the same description are given a new unique value. To the moment, table2style only exports geotiff rasters.

The plugin is available in a GIT repository.. To install, just copy a folder "table2style" with all files to your QGIS plugin folder. This folder is usually found in "YOUR_HOME_DIR/.qgis/python/plugins" but check this site for additional details. Inside QGIS you can find the plugin listed in the plugin manager.

(last updated: 05-Oct-2015)