Visualize population genomics analyses results

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Documentation for package ‘sgtr’ version 1.1.2

Help Pages

assign_defaults Assign default values to a track object
assign_values Assign value to track property
check_highlight_sectors Check highlighted sectors
cluster_marker_depths Cluster marker depths data
configure_backgrounds Configure sector background colors
configure_track Configure track data from default values
convert_to_kb Convert position to Kb
convert_to_mb Convert position to Mb
create_palette Create bias color palette
create_track_data Create track data
detect_chromosomes Detect chromosomes
draw_barplot Draw a barplot for a metric
draw_boxplot Draw a boxplot for a metric
draw_circos Draw genome metrics in a circular layout
draw_circos_track Plot a circos track
draw_density Draw density for a metric
draw_distrib Draw a tile plot for radsex "distrib" results
draw_manhattan_plot Draw genome metrics in a manhattan plot
draw_manhattan_track Plot a manhattan track
draw_marker_depths RADSex marker depths plot
draw_region Draw genome metrics for a specified genomic region
draw_region_track Plot a region track
drop_columns Drop columns from a data frame
generate_color_palette Generate a color palette for "distrib" plot
generate_x_scale Generate x-axis scale
generate_y_scale Generate y-axis scale
get_contig_lengths_from_data Get contig lengths from genome metrics data
h_line Create a h_line object
load_chromosome_names Load chromosome names
load_genome_metrics Load a genome metrics data file
load_group_info Load group info
load_marker_depths Load a standard table file
load_marker_distribution Load a marker distribution table
load_table Load a standard table file
manhattan_bg_colors Assign color to manhattan background data
metric Create a metric object
multi_metrics_track Create a track object with multiple metrics
open_output_device Open output device
parse_region Parse region
plot_circos Plot genome metrics in a circular layout
plot_manhattan Plot genome metrics in a manhattan plot
plot_region Plot genome metrics for a specificied genomic region
radsex_depth Plot the results of radsex "depth" analysis
radsex_distrib Plot the results of radsex "distrib" analysis
radsex_freq Plot the results of radsex "freq" analysis
radsex_map_circos RADSex circos plot
radsex_map_manhattan RADSex manhattan plot
radsex_map_region RADSex region plot
radsex_marker_depths Plot the results of radsex "subset", "signif", or "process"
read_comments Parse comment lines in an input file
single_metric_track Create a track object with a single metric
track Create a track object