Man pages for thackl/thacklr
A Collection of R Functions and Snippets I Often Use.
| ancestor | Compute the ancestor of a gff feature |
| as.multiPhylo.list | Convert a List into multiPhylo Object |
| clean_tips | Remove Missing Tips |
| distance | Compute great circle distances |
| enable_TODO | Enable/Disable TODO() messages |
| flip_descendants | Flip Descendant Clades |
| get_children | Get Child Nodes |
| gg_color_hue | ggplot default color vector |
| ggtreeplot | Create a ggplot next to a ggtree |
| index_by | Index by keys preserving order |
| mount_mit | Mount MIT remote drives |
| no_grid | Remove grid from ggplot |
| no_legend | Remove legend from ggplot |
| no_x_axis | Remove x-axis from ggplot |
| no_y_axis | Remove y-axis from ggplot |
| pkg_update | Document and reload dev package |
| prune_long_tip_branches | Prune very long branches |
| qw | Create a vector from unquoted words. |
| read_bed | Read a .bed file |
| read_blast | Read a BLAST .tsv files |
| read_eggnog | Read EggNOG-mapper annotation .tsv files. |
| read_fai | Read fasta index |
| read_gff | Read a .gff file |
| read_hmmer | Read a HMMER .tbl/tsv file |
| read_interpro | Read InterProScan .tsv files. |
| read_paf | Read a .paf file (minimap/minimap2). |
| reexports | Objects exported from other packages |
| reroot_by_outgroup | Reroot Tree by Outgroup |
| scale_y_tree | Continious y-scale with fixed expansion space |
| session_info_diff | Compare sessionInfo()s |
| set_class | Modify object class attriutes |
| split_by | Split by key preserving order |
| str_which_unique | Keep strings uniquely matching a pattern, or find positions. |
| TODO | Add TODO statements. See 'enable/distable_TODO' for control... |
| tree_y | Get tree-based y-coordinates |
| tree_ylim | Get the range of the ggtree y-axis data |
