Man pages for k-hench/GenomicOriginsScripts
Provides the R scripts for the paper "Ancestral variation, hybridization and modularity fuel a marine radiation"
| add_gpos | Add genomic position |
| add_spec_drawing | Add fish annotation |
| adm_plot | Plot adimxture data |
| anno_pair_flag | create hamlet pair annotations |
| as_multirow | Wrap content in multirow |
| ax_scl | Scale bp to Mb |
| bammplot_k | A modded version of BAMMtools::plot.bammdata |
| clr | Hamlet colors (standard) |
| clr2 | Hamlet colors (alternative) |
| clr_below | Default background bar color |
| clr_genes | Default gene color |
| clr_loc | Location colors |
| collapse_peaks | Collapse all Fst peaks of a given run |
| conditional_highlight | Conditional Tree Highlighting |
| conditional_rotate | Conditional Tree Rotation |
| cross_spec | Cross species pairs |
| custom_annoplot | Custom annotation base plot |
| darken | Darken a given color |
| data_amdx | Get adimxture data |
| distances_tree | Get distance matrix of a topology |
| dist_tibble | Create tibble of pairwise species distances |
| dot-onAttach | Package Dependencies |
| export_2_latex | Export latex tables |
| fish_plot | hamlet pair annotation |
| fish_plot2 | hamlet pair annotation 2 |
| fll_fun | Fill function for adxiture classes |
| fll_n | Named fill function for adxiture classes |
| fst_bar_row_run | crate global fst bar table |
| f_width | Default figure width (double column) |
| f_width_half | Default figure width (single column) |
| generic_hamlet_img | Generic Hamlet image. |
| geom_hypo_grob2 | The custom grob geom |
| get_cc | Import cross coalescence data |
| get_clr | Defin topology weighing base color |
| get_dist | Create distance of species pair |
| get_dxy | Import dxy data |
| get_fst | Import Fst data |
| get_fst_fixed | Compute summary stats an absolute for Fst outlier |
| get_fst_summary_data | Import fst summary data for outlier windows |
| get_genes | Collect hamlet genes |
| get_gxp | Import genotype x phenotype association |
| get_gxp_and_geva | Combine allele age and gxp data import |
| get_gxp_both_models | Get gxp data |
| get_gxp_long | Import genotype x phenotype association in long format |
| get_isolated_topos | get isolated topologies |
| get_msmc | Import msmc data |
| get_n_above | Count number of permutation Fst greather than the original... |
| get_neighbour_topos | Get pairwise highlighing topologies |
| get_n_total | Count number of fst permutations |
| get_percentile | Compute the percentile of original Fst copared to fst... |
| get_pi | Import diversity data |
| getPofZ | Get hybridization data |
| get_random_fst | Import Fst permutation tests results |
| get_twisst_data | Import a single topology weighting data set |
| grid_piece_x | Single grob annotation for specific x range |
| gxp_importer | Import windowed gxp data for focal trait |
| hypo_anno_l_lwd | Hamlet Annotation (alt) |
| import_geva_data | Import Geva data (Allele Age) |
| import_gxp_data | Import windowed gxp data for all traits |
| import_tree | Import revPoMo tree |
| is_isolated | Determine if species is isolated in topology |
| join_list | Iterate left_join over list |
| lab2spec | Convert tree labels |
| label_spacer | Adjust plot sizes |
| lighten | Lighten a given color |
| loc_names | Location names |
| make_faint_clr | make a faint version of a color |
| match_twisst_files | Import all topology weighting data sets for a location |
| min_dist | Find minimum distance to other species in topology |
| network_layout | crate a network layout for pairwise species comparisons |
| no_title | drop ggplot y axis titles |
| outlr_clr | Outlier color |
| pca_plot | Automated PCA plotting |
| pca_plot_no_fish | PCA plot without fish annotations |
| plot_clr | Default plot color |
| plot_curtain | Manage plot panels for a single outlier window |
| plot_fish | Plot single fish |
| plot_fish2 | Plot Hamlet drawing (alt) |
| plot_fishes_location | Plot two fishes with location |
| plot_fish_lwd | Hamlet Annotation (alt) |
| plot_fish_zoom | Plot fish for topology legend |
| plot_fst_poptree | Create the fst population tree panel |
| plot_leg | Create topology legend |
| plot_loc | Plot hybridization data |
| plot_lwd | Default plot linewidth |
| plot_network | Plot pariwise species comparisons per location |
| plot_outl_tree | plot region tree |
| plot_outl_tree_s | plot region tree (with Serranus outgroup) |
| plot_pair_run | create hamlet pair annotations |
| plot_panel_anno | Create annotation panel |
| plot_panel_delta_dxy | Create the delta dxy panel |
| plot_panel_dxy | Create the dxy panel |
| plot_panel_fst | Create the fst panel |
| plot_panel_gxp | Create the genotype x phenotype panel |
| plot_panel_twisst | Create the topology weighting panel |
| plot_size | Default plot size |
| plot_text_size | Default plot font size |
| plot_text_size_small | Small plot font size |
| plot_tree | Plot Tree |
| pop_levels | Population order |
| prep_data | Prepate topology weighting data for zoom plot |
| process_input | Process script input |
| project_case | Project case |
| project_inv_case | Inverted project case |
| read_sc | import sc data sheet |
| refactor | Reorder factor levels |
| refactor_run | reorder species pairs |
| reformat_run_name | Reformat run name |
| rescale_fst | normalize global fst |
| reverselog_trans | Custom reverse log transformation |
| root_hamlets | Root hamlet tree |
| shps | Location shapes |
| sp_labs | Species labels |
| sp_names | Species names |
| summarise_model | summarize model statistics |
| summarize_dxy | Import and summarize dxy data |
| summarize_fst | Import and summarize Fst data |
| theme_gradient_bg_x | Tiled Grob background for ggplot |
| theme_hyb | Custom ggplot theme |
| theme_panels | ggplot layout template |
| whisker_points | Whisker points |
