CHANGELOG.md

In lmc297/bactaxR: Bacterial taxonomy construction and evaluation in R

bactaxR CHANGELOG

All noteable changes to bactaxR will be documented in this file

[0.2.3] 2024-01-30

Added

• Added the ability to specify any hclust agglomeration method in ANI.dendrogram (default is "average", which was previously hard-coded as the hclust method).

[0.2.2] 2022-10-06

Added

• Added ladderize and ladderize_right parameters to the phylo.discrete_trait_OTU function.

[0.2.1] 2022-06-03

Added

• Added font_angle and font_offset_y parameters to the phylo.discrete_trait_heatmap function.

[0.2.0] 2022-05-29

Changed

• Fixed legend color order bug in ANI.graph function; in bactaxR v0.1.0, ANI.graph would assign colors to graph nodes by converting user-supplied metadata to a factor, converting resulting factors to numeric values, and then supplying the color palette with the numeric values, i.e., vertex.color = color_palette[as.numeric(as.factor(vertex_attr(ig, "species")))],. This resulted in colors in the legend sometimes not matching the plotted colors. To correct this, ordered levels are now explicitly used, i.e., vertex.color = color_palette[as.numeric(factor(vertex_attr(ig, "species"), levels = sorted_labels))], where sorted_labels <- unique(vertex_attr(ig, "species")).

[0.1.0] 2020-01-24

Added

• Initial commit

lmc297/bactaxR documentation built on Feb. 6, 2024, 7:41 p.m.