mapmixture v1.2.0

• Feature. The pie_size argument now accepts a single value or a vector of values the same length as the number of sites. This allows users to plot pie of different sizes for different sites.

• Issue #28. Changing the order of items in the legend. Fixed an issue when there are 10 or more clusters named cluster1, cluster2, ..., cluster10, clusterN. The main change is in the func_process_input_data.R script, whereby the renaming of cluster columns is now cluster01, cluster02, ..., instead of cluster1, cluster2, ..., to make sure the order is the same as the input.

• Shiny app. Package dependencies for the Shiny app only are now on the Suggest list of dependencies rather than the Imports list. When launch_mapmixture() is executed, the function will check the dependencies are installed or ask the user to install them.

• Structure plot. A permanent change in the default plotting of individuals on the structure plot. Previously, the individual column was sorted alphabetically, but users have indicated it is more ideal to preserve the original order of individuals for each site in the admixture data file. This is now the default behaviour for structure_plot().

mapmixture v1.1.4

Updates

• Added arguments to change the border colour and size of polygons (#18):
  basemap_border = TRUE, basemap_border_col = "black", basemap_border_lwd = 0.1.

• Added argument to not display site labels in structure plot:
  display_site_labels = FALSE.

• Changed R dependency to address issue #23.

mapmixture v1.1.3

Updates

• Add argument site_labels_angle to optionally change the angle of the site labels in admixture structure plots (#15).
• Fix to #16 where the size of single-coloured pies (circles) were smaller than multi-coloured pies. This occured when the admixture file format 1 contained both fixed genotypes (0 and 1 for a cluster) and admixed genotypes (e.g. 0.5, 0.25, 0.25).
• Changed the default pie size when coordinate reference system is WGS 84 (EPSG:4326) to be more like the pie sizes of projected coordinate reference systems.
• Add argument pie_border_col to optionally change the colour of the pie segment borders.

mapmixture v1.1.2

Updates

• To comply with CRAN policy, the high resolution basemap originally distributed with mapmixture v1.1.1 has been replaced with the medium resolution basemap distributed with the rnaturalearthdata package, which mapmixture now imports as default for the mapmixture() function. See the mapmixture GitHub example page for the single line of code needed to import the high resolution basemap from the rnaturalearthhires package.
• Added extra arguments to customise scatter plot site divider lines.
• Minor updates to documentation.

mapmixture v1.1.1

Updates

• Stable release available to install through CRAN with install.packages("mapmixture").
• Small improvements to description and documentation.
• Some minor improvements to the interactive app.

mapmixture v1.1.0

Main updates

• mapmixture now distributed as an R package.
• Additional functions have been added to create structure admixture plots and scatter plots based on PCA or DAPC results.
• Improvements to the creation and rendering of pie charts on the map.
• Users can use their own vector or raster data as the basemap in mapmixture.

Minor updates

• Improvements to Shiny app layout and validation.
• Reduced dependency on scatterpie by using custom code to generate and render pie charts.

Mapmixture v1.0.4

Main updates

• Coordinate reference system (CRS) input selector now has categories for projections, e.g. Africa, Europe, Pacific Ocean, etc. (see image below)
• A border input option for the thickness of pie chart outlines
• Code improvements and updating several R packages

Mapmixture v1.0.3

Summary
This release fixes bugs with uploading data and adds default cluster colours to pie charts.

Main updates

• Fix issue with cluster column names when uploading admixture file. Previously, if cluster columns when not named "Cluster 1, Cluster 2, Cluster ..., Cluster N", the app crashed. Now, users can name cluster columns anything and this will be plotted as the cluster labels on the map.
• Add default cluster colours to pie charts. Previously, all pie charts were rendered as white. Now, a green-blue palette is rendered by default depending on the number of clusters in the admixture data. To do this, map2() has been superseeded by pmap() in the R code.

Minor updates

• Update rhino package to version 1.4.0.
• Replace magnittr pipe with native R pipe.
• Remove redundant R code and script(s).
• Add a little bit of space right of the Plot Map button (increase padding-right by 5px in scss).

Mapmixture v1.0.2

Summary
This release updates all numeric inputs to have a minimum value of zero and adds information to the file format documentation.

Detail

• All numeric inputs now have a minimum value of zero
• The pie chart opacity numeric input has a maximum value of one
• Added that headers are required in both input files in the file format documentation

Mapmixture v1.0.1

Summary
This release fixes crashing of the app when admixture or coordinates files are uploaded with column headings that are different from the ones expected by ggplot. Users can now upload files with any column name and these will be converted after files have been successfully parsed.

Detail

• Users can upload admixture file with any names for column headings (i.e. Site, Individual and Cluster columns)
• Users can upload coordinates file with any names for column headings (i.e. Site, Lat and Lon columns)