Package index • ezGenomeTracks

Core Functions

Main functions for creating genomic tracks

ez_coverage(): Easy coverage track visualization

ez_feature(): Easy peak track visualization

ez_gene(): Easy gene track visualization

ez_link(): Easy interaction track visualization

ez_sashimi(): Easy sashimi plot visualization

ez_manhattan(): Easy Manhattan plot visualization

ez_hic(): Easy Hi-C track visualization

vstack_plot(): Stack multiple genome tracks

hstack_plot(): Stack multiple plots horizontally

Geom Functions

Low-level geometric objects for genomic data

geom_coverage(): Coverage visualization geom

geom_feature(): Geom for genomic feature tracks

geom_gene(): Geom for gene model tracks

geom_link(): Geom for genomic interaction links

geom_manhattan(): Create a Manhattan plot

geom_hic(): Geom for Hi-C contact matrix visualization (square heatmap)

geom_hic_triangle(): Geom for Hi-C contact matrix visualization (triangle/rotated view)

Data Processing Functions

Functions for importing and processing track data

process_signal_input(): Process signal input into standardized data frame

process_gene_data(): Process gene annotation data for visualization

process_interaction_data(): Process interaction data for visualization

process_sashimi_data(): Process sashimi plot data for visualization

process_sashimi_input(): Process sashimi plot input into standardized data frames

process_manhattan_input(): Process Manhattan plot input into standardized data frame

process_hic_data(): Process Hi-C data for visualization

import_genomic_data(): Import genomic data from a file into a tidy data frame

interaction_track(): Create an interaction track from a file

Themes and Scales

Functions for customizing track appearance

ez_theme(): A minimal theme for genome track visualization

ez_coverage_theme(): A theme for coverage tracks

ez_feature_theme(): A theme for feature tracks

ez_gene_theme(): A theme for gene tracks

ez_sashimi_theme(): A theme for sashimi plots

ez_manhattan_theme(): A theme for Manhattan plots

ez_hic_theme(): Hi-C theme

scale_x_genome(): Scale for genomic coordinates on the x-axis

scale_x_genome_region(): Create a genomic position scale for a specific chromosome region

scale_y_strand(): Y-axis scale for strand tracks

scale_fill_hic(): Scale for Hi-C contact matrix fill colors

hic_palette_cooler() hic_palette_ylgnbu() hic_palette_viridis() hic_palette_bwr(): Hi-C color palettes

Annotation Functions

Functions for adding annotations to tracks

add_vline(): Add a vertical line to a genome track

add_hline(): Add a horizontal line to a genome track

add_rect(): Add a rectangle to a genome track

add_text(): Add text annotation to a genome track

Helper Functions

Utility functions for data conversion and calculation

granges_to_df(): Convert a GRanges object to a tidy data frame

df_to_granges(): Convert a data frame to a GRanges object

parse_region(): Parse a genomic region string into a GRanges object

format_genomic_coord(): Format genomic coordinates

extract_txdb_data(): Extract gene data from TxDb object

get_single_signal(): Extract signal data for a single input element

plot_signal_df(): Plot signal tracks from a data frame with grouping

calculate_link_ylim(): Calculate y-axis limits for link tracks

stat_bin_signal(): Stat for binning genomic signal data

Example Datasets

Example datasets for demonstration

example_signal: Example signal data

example_peaks: Example peak data

example_genes: Example gene data

example_interactions: Example interaction data

example_junctions: Example splice junction data for sashimi plots

example_hic: Example Hi-C data