Man pages for djw533/micro.gen.extra
Microbial genomics extensions and functions
| add_clades_to_tree | Highlight clades over a ggtree object given a named vector of... |
| collapse_tree | Collapse a set of nodes in a ggtree object |
| create_blast_comparisons | Create blast comparisons for synteny plots |
| create_dnaseqs | Create a dnaseqs list of dataframes for genoplotR |
| create_upset_dfs | Create UpSetR dataframes from a gene_presence_absence.Rtab... |
| fasta_from_gff_list | Get fasta sequence from several single-contig gff3 file |
| fasta_from_single_gff | Get fasta sequence from single-contig gff3 file |
| fasta_len_from_single_gff | Get fasta length from single-contig gff3 file |
| fasta_lengths_from_gff_list | Get fasta sequence from several single-contig gff3 file |
| fasta_to_df | Read in sequence data and fasta header from a fasta file into... |
| flip_gggenes | Flip and/or centre gggenes data |
| get_clade_nodes | Find internal clade nodes ancestral to named/numbered sets of... |
| get_intersect_members | Get members (genes) of a set intersection shown in an UpsetR... |
| get_within_species_cluster_mrcas | Find internal clade nodes ancestral to named/numbered sets of... |
| gggenes_df_from_gff_dir | Create a dataframe for input to gggenes from a directory of... |
| gggenes_df_from_gff_file | Create a dataframe for input to gggenes from a single gff3... |
| gggenes_df_from_gff_list | Create a dataframe for input to gggenes from a list of gff3... |
| gheatmap_with_gaps | Put a multi-column gheatmap onto a ggtree object with gaps... |
| is.hex | Hexcode colours (from Glimma v1-hexcol.R) |
| nested.test.check | Compare two lists of lists for nested items |
| parse_interproscan_gff | Parse interproscan gff3 file to a dataframe |
| parse_snpEff_vcf | Parse snpEff output into tidy dataframe |
| plot_gene_accumulation_curves | Plot gene accumulation curves |
| plot_genoplot_data | Plot a genoplotR synteny plot |
| plot_genoplotR_key | Plot the key for a genoplotR synteny plot |
| plot_hamburger | Plot hamburger results for each strain |
| plot_synteny_gff_files | Take a list of "x" gff3 files and create a synteny plot |
| plot_t6_clusters | Plot T6SS hamburger results for each strain |
| protein_from_sequence | Translate protein sequences from a corresponding fasta... |
| random_n_colours | Create a vector of "n" random colours |
| read_gff | Read in annotation from gff file into a tidy dataframe |
| remove_tips_from_tree | Prune a list of tips from a tree |
| reverse_gff | Reverse a gff file |
| run_cdhit | Run CDhit on a list of protein sequences |
| run_hmmsearch | Run Hmmsearch |
| snippycore_to_df | Read in snippy-core alignment into tidy dataframe for... |
| subsample_tree | Subsample a phylogenetic tree |
