Function reference
Adding geological timescales to plots
The original purpose of deeptime, coord_geo() adds a highly customizable timescale to any ggplot2 plot. Other functions now supplement it to aid in the visualization of data over long time scales.
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coord_geo() - Transformed coordinate system with geological timescale
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scale_color_geo()scale_fill_geo()scale_discrete_geo() - Geological Time Scale color scales
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get_scale_data() - Get geological timescale data
Built-in interval data
deeptime includes a selection of built-in interval data from the most up-to-date Geological Time Scale. These dataframes include name, max age, min age, abbreviation, and color columns.
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eons - Eon data from the International Commission on Stratigraphy (v2022/10)
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eras - Era data from the International Commission on Stratigraphy (v2022/10)
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periods - Period data from the International Commission on Stratigraphy (v2022/10)
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epochs - Epoch data from the International Commission on Stratigraphy (v2022/10)
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stages - Stage data from the International Commission on Stratigraphy (v2022/10)
Deprecated functions
The following functions represent the first and second iterations of what is now coord_geo(). These functions still work but are considered “deprecated”. There is no plan to remove them in the immediate future (for those who used them or still use them in their code), but there is no guarantee they will be supported ad infinitum. Users are strongly encouraged to use coord_geo() instead, which has more features and is still under active development.
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gggeo_scale()print(<geo_scale>) - Add a geologic scale below ggplots using grid
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gggeo_scale_old() - Add a geologic scale on top of ggplots
Adding geological timescales to phylogenies
These functions can be used to add timescales specifically to phylogenies that are plotted with ggtree.
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coord_geo() - Transformed coordinate system with geological timescale
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coord_geo_radial() - Enhanced polar coordinate system with geological timescale
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coord_geo_polar() - Polar coordinate system with geological timescale
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scale_color_geo()scale_fill_geo()scale_discrete_geo() - Geological Time Scale color scales
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get_scale_data() - Get geological timescale data
Transforming coordinate systems
These functions can be used to modify the way that your data is plotted by ggplot2.
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coord_trans_flip() - Transformed and flipped Cartesian coordinate system
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coord_trans_xy() - Transformed XY Cartesian coordinate system
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geom_phylomorpho() - Plot a 2-D phylomorphospace in ggplot2
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disparity_through_time() - Disparity through time plot using lattice
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panel.disparity() - Combined wireframe and cloud panel
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coord_trans_xy() - Transformed XY Cartesian coordinate system
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geom_points_range()stat_points_range() - Display points and their range
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facet_grid_color() - Lay out panels in a grid with colored strips
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facet_wrap_color() - Wrap a 1d ribbon of panels into 2d with colored strips
Combining and arranging plots
These functions can be used to combine and arrange plots into publishable-quality figures.
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ggarrange2() - Combine and arrange multiple ggplot-like objects
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gtable_frame2() - Decompose a ggplot gtable