2.7.5

update renv lockfile for R v4.1.0

2.7.2

recompressed example data

2.7.0

Overhauled amp_load()

2.6.8

remove return() from pipe

2.6.6

uptick version 2.6.6 + rerun docs

2.5

CBA, see commits for now!

2.4.0

Most important changes

• amp_alphadiv:Added a RawReads column when rarefy is set
• amp_heatmap: Functions dual plot now returns an object with a custom print class so that it is possible to manipulate each plot with regular ggplot2 syntax before the dual plot is printed
• amp_heatmap: Updated functional data from midasfieldguide.org for the functions dual plot
• amp_ordinate: Added a caption generator to show exactly what produced the ordination plot, with references for each distance measure and transformation etc
• amp_rarecurve: Added faceting to split the plot
• amp_rankabundance: Fixed appearance when plot is generated per sample (ungrouped)
• Fixed axis titles in amp_timeseries + amp_boxplot + amp_core + amp_rankabundance when data has not been normalised
• amp_ordinate: Fixed an issue where trajectory didn't show correctly without a trajectory group defined
• amp_alphadiv: Fixed an issue where an error occured if data only has 1 sample

Miscellaneous

• Added a trajectory example with amp_ordinate to get started guide
• Updated phylogenetic tree in the AalborgWWTPs example data

2.3.11

Functions

Added two new import functions

• amp_import_biom for importing data in the BIOM format (fe06eef)
• amp_import_usearch to import data from the usearch10 pipeline command family (fe06eef)

amp_heatmap

• Added functions_legend_text_size and functions_axis_text_size to adjust legend and axis text sizes when the MiDAS functions sideplot is enabled (90489ac)
• Fixed a bad condition when sort_by is used resulting in incorrect sorting (8b28129)
• normalise_by wasn't working as intended, now using data.table instead of tidyr (c8ab464)

amp_timeseries

• Fixed a bug when group_by == NULL with the ggplot2 dev version 2.2.1.9000 (7d39d5c)
• Added an option scales to set the y-axis scales to fixed or free, when split == TRUE (99b88fe)
• Corrected the y-axis title to match if the data has been normalised or not (5c803a5)

amp_export_otutable

• Added file extension argument to the exported text file (ca8a7b6)

amp_ordinate

• Adjusted metadata hover information when sample_plotly is enabled (344b71f)
• Fixed a bug with color_by and shape_by with the ggplot2 dev version 2.2.1.9000 (0a86823)
• Fixed a bug where envfit in amp_ordinate with PCoA did not work (df1c3f5)

amp_subset_samples

• Added a rarefy option (8ad8955)

Documentation and webpage

• Added a search field to the webpage (c7f41c4)
• Adjusted the get started guide in particular how to load data (3122f70)
• Changed citation to the bioRXiV paper
• Added links to albertsenlab.org blog posts (3122f70)
• Added GitHub issue template (f1fb824)
• Added google analytics integration to webpage (e572172)
• Added "see also"s to several functions (3122f70)

Additional bug fixes

• Fixed a bug where c__ was added to phylum names instead of p__ when 'tax_empty == "best"` (509f9a4)

2.3.3

General

• Renamed raw to normalise in all plotting functions. If the data is already normalised and normalise = TRUE then a warning is shown
• Fixed a bug when the data was normalised with only one sample

amp_heatmap

• Fixed a bug with textmap when plot_functions = FALSE

amp_subset_taxa

• Now shows a short summary of the subset just like amp_subset_samples does

amp_ordinate

• Added envfit_arrowcolor to color the arrows when doing numerical fitting

Under the hood

• All imports converted to importFrom to avoid warning spam and to only load functions that are actually used.
• Added call. = FALSE in all warning and error messages
• Read stats are now stored as an attribute in the ampvis2 object when the data is normalised with either amp_subset_samples or amp_subset_taxa. In this way it will print correctly with print.ampvis2 and not just show 100 everywhere, but manual editing the data will probably cause the stats to be incorrect from now on
• ampvis2 objects printed to the console now has underlined section titles
• Both amp_subset_samples and amp_subset_taxa now also checks if the data has already been normalised

2.3.0

amp_heatmap

• amp_function has been integrated into amp_heatmap
• Fixed the sort_by argument to now work on both a sample or a group (not both)

amp_load

• Values with NA or "" in the otutable introduced bugs, they are now converted to 0's

amp_ordinate

• Using a custom distance matrix is now possible, described on the ampvis2 FAQ

amp_otu_network

• Now working as intended

Bug fixes:

• Fixed an issue where a sample with 0 reads after a subset caused trouble in functions where the read abundances are normalised. Division by 0 logically results in NaN, but caused trouble.
• #19
• #31
• #32
• #33
• #35
• Minor adjustments