v2.2.1

What's Changed

• Development by @KasperSkytte in #36

New Contributors

• @KasperSkytte made their first contribution in #36

Full Changelog: 2.1.3...v2.2.1

2.1.3

Includes new function mmheatmap() and more.

2.0.7 without Rtsne

version 2.0.7 without Rtsne

2.0.7

General

• Added PCA of tetra-nucleotide frequences to the example data mmgenome2
• Added a custom print method for ggplot objects that suppresses ALL messages. This means the print_plot argument has been removed everywhere.

Functions

New function: mmmerge_linkfiles

Searches a folder for all files with a filename ending with _link, and then all the files found are loaded and merged into one data frame. This is done by searching the files for all unique scaffold pairs and summing the number of connections per pair. The files must contain 3 columns called "scaffold1", "scaffold2", and "connections".

mmload

• Added a status message of the loaded coverage files when scanning a folder for coverage files.

mmcov_profiles

• normalise set to FALSE by default

mmstats

• The numbers are now aligned at the decimal point for pretty printing and the numbers are separated by a whitespace for every 3 digits to make it easier to read quickly.
• Added an option to also provide the original data of which the data is a subset to compare the relative coverage contribution to the original data

mmplot_pairs

• GC content as well as all coverage profiles are now default axes unless otherwise set

mmnetwork

• Now shows a meaningful error message when there are no connections between the scaffolds

Bug fixes

• mmlocator quosure bug
• The marked selection is now just copied to clipboard without asking

Documentation and webpage

• Added installation instructions for mmgenome2 with R version 3.5.0 for MAC
• Fixed some broken relative URLs on webpage
• Added google analytics integration

2.0.4

Installation

• Installation adjusted to work with remotes::install_github() instead of biocLite(), which rarely works without problems.
• Replaced dependency Rtsne.multicore with Rtsne@openmp as the former is not actively developed anymore
• Tested installation on MAC by an installation guide on website

mmload()

• Now checks for duplicate scaffold names in coverage, taxonomy, and additional, error if duplicates found

mmplot()

• Added factor_shape argument to shape scaffolds as circles when color_by is categorical

Documentation website

• Added a search field
• Added and tested MAC installation guide
• Introduction to mmgenome2 updates
• Fixed bad links
• Various updates and adjustments

Other

• Adjusted function examples
• Added print_plot argument to mmplot(), mmplot_cov_profiles(), and mmplot_pairs() to suppress warnings so they print the plot rather than return a ggplot object, default: TRUE.
• Added github issue template
• Various bug fixes and future-proof testing as well as changes to code behind the scenes that do not affect the end user

First release of mmgenome2

2.0

mmstats returned NA if some scaffolds were missing coverage