Man pages for trvinh/test
PhyloProfile
| calc_pres_spec | Calculate percentage of present species in each ortholog... |
| calculate_p_value | calculate the p_values |
| check_input_validity | Check the validity of the main input file |
| check_newick | Check the validity of input newick tree |
| check_oma_id | Check OMA IDs |
| cluster_data_dend | Create a dendrogram tree from the distance matrix |
| create_archi_plot | Create protein's domain architecure plot |
| create_domain_df | Create domain annotation dataframe for one OMA protein |
| create_gene_age_plot | Create gene age plot |
| create_long_matrix | Create a long matrix format for all kinds of input file |
| create_percentage_distribution_data | Create data for percentage present taxa distribution |
| create_profile_data | Create data for plotting the phylogentic profiles |
| create_profile_from_oma | Create phylogenetic profile from a raw OMA dataframe |
| create_rooted_tree | Create rooted tree from a taxonomy matrix |
| create_var_dist_plot | Create distribution plot |
| create_variable_distribution_data | Create data for additional variable distribution |
| create_variable_distribution_data_subset | Create data for additional variable distribution (for a... |
| data_customized_plot | Create data for customized profile plot |
| data_main_plot | Create data for main profile plot |
| domain_plotting | Create architecure plot for a single protein |
| estimate_gene_age | Calculate the phylogenetic gene age from profiles |
| fasta_parser | Parse multi-fasta input file |
| from_input_to_profile | Create data for plotting profiles (from raw input to final... |
| full_processed_profile | An example of a fully processed phylogenetic profile. |
| full_processed_profile_large | An example of a large processed phylogenetic profile. |
| gene_age_plotDf | Create data for plotting gene ages |
| get_all_domains_oma | Create domain annotation dataframe from a raw OMA dataframe |
| get_all_fasta_oma | Get all fasta sequences from a raw OMA dataframe |
| get_common_ancestor | Generate the in_group |
| get_core_gene | Identify core genes for a list of selected taxa |
| get_data_clustering | Get data for calculating the distance matrix |
| get_data_for_one_oma | Get OMA info for a query protein and its orthologs |
| get_data_for_one_ortholog | Get taxonomy ID, sequence and annotation for one OMA sequence |
| get_dendrogram | Plot dendrogram tree |
| get_distance_matrix | Calculate the distance matrix |
| get_domain_file | Get domain file from a single (concatenate) file |
| get_domain_folder | Get domain files from a folder |
| get_domain_from_url | Get domain annotation from OMA Browser |
| get_domain_online | Get domain file(s) for online data set |
| get_fasta_seqs | Get fasta sequences |
| get_features | get the list with all the features in the gene |
| get_ids_rank | Get taxonomy info for a list of taxa |
| get_input_taxa_id | Get ID list of input taxa from the main input |
| get_input_taxa_name | Get NCBI taxon names for a selected list of taxa |
| get_name_list | Get list of pre-installed NCBI taxon names |
| get_oma_members | Get OMA members |
| get_prefix_features | Get the database for each feature in a specific gene |
| get_p_values | Decide if the gene is significant |
| get_qual_col_for_vector | Get color for a list of items |
| get_selected_fasta_oma | Get selected fasta sequences from a raw OMA dataframe |
| get_selected_subset | Get the subset depending on the choosen rank |
| get_significant_genes | Get the dataframe with the significant genes |
| get_taxonomy_matrix | Get taxonomy matrix |
| get_taxonomy_ranks | Create a list with all main taxanomy ranks |
| heatmap_plotting | Create profile heatmap plot |
| highlight_profile_plot | Highlight gene and/or taxon of interest on the profile plot |
| main_long_raw | An example of a raw long input file. |
| parse_domain_input | Parse domain input file |
| parse_info_profile | Parsing info for phylogenetic profiles |
| pp_taxonomy_matrix | An example of a taxonomy matrix. |
| pp_tree | An example of a taxonomy tree in newick format. |
| profile_with_taxonomy | An example of a raw long input file together with taxonomy... |
| qualitative_colours | Create qualitative colours |
| rankIndexing | Indexing all available ranks (including norank) |
| reduce_profile | Reduce the full processed profile into supertaxon level |
| run_phyloprofile | Run PhyloProfile app |
| search_taxonID_online | Search NCBI taxonomy IDs for a list of taxon names |
| sort_domains | Sort one domain dataframe based on the other domain dataframe |
| sort_input_taxa | Sort list of (super)taxa based on a selected reference... |
| sort_taxa_from_tree | Get sorted supertaxon list based on a rooted taxonomy tree |
| str_reverse | Reverse string |
| taxa2dist | TAXA2DIST |
| taxa_select_gc | print list of available taxa |
| taxonomy_table_creator | Align ncbi taxonomy IDs of all taxa into a sorted rank list |
| wide_to_long | Transform input file in wide matrix into long matrix format |
| xml_parser | Parse orthoXML input file |
