rnavigate.plots.functions package
Submodules
rnavigate.plots.functions.circle module
- rnavigate.plots.functions.circle.plot_annotation_circle(ax, seq_circle, annotation, offset=1)
Plot annotations on a circle plot.
Parameters
- axmatplotlib.axes.Axes
The axes to plot on.
- seq_circlernavigate.data.SequenceCircle
The sequence circle object containing nucleotide positions.
- annotationrnavigate.data.Annotation
The annotation to be plotted.
- offsetfloat, optional
The offset from the circle circumference to plot the annotation.
- rnavigate.plots.functions.circle.plot_interactions_circle(ax, seq_circle, interactions)
Plot interactions on a circle plot.
Parameters
- axmatplotlib.axes.Axes
The axes to plot on.
- seq_circlernavigate.data.SequenceCircle
The sequence circle object containing nucleotide positions.
- interactionsrnavigate.data.Interactions
The interactions to be plotted as arcs between nucleotides.
rnavigate.plots.functions.functions module
- rnavigate.plots.functions.functions.adjust_spines(ax, spines)
Places the given spines on the given axis, removes others.
Parameters
- axmatplotlib.axes.Axes
The axes to adjust the spines of.
- spineslist of str
The spines to adjust. Valid options are “left”, “right”, “top”, and “bottom”.
- rnavigate.plots.functions.functions.box_xtick_labels(ax)
Place a transparent box behind the xtick labels of the provided axis.
- rnavigate.plots.functions.functions.clip_spines(ax, spines)
Clips the given spines to the range of the ticks.
Parameters
- axmatplotlib.axes.Axes
The axes to clip the spines of.
- spineslist of str
The spines to clip. Valid options are “left”, “right”, “top”, and “bottom”.
- rnavigate.plots.functions.functions.get_contrasting_colors(colors)
Get contrasting colors for a list of colors.
Returns a list of “k” (black) or “w” (white) for each color in the input list, which ever contrasts better with the input color.
Parameters
- colorslist of str
List of colors to get contrasting colors for.
Returns
- list of str
List of “k” or “w” for each color in the input list.
- rnavigate.plots.functions.functions.get_nt_ticks(sequence, region, gap)
Get the ticks and labels for a region of a sequence.
Dashes are ignored when counting nucleotide positions.
Parameters
- sequencestr or rnavigate.data.Sequence
The sequence to get ticks and labels for.
- regiontuple of int
The region of the sequence to get ticks and labels for.
- gapint
The gap between major ticks.
Returns
- ticks, labelstuple of list of int
The ticks and labels for the given region of the sequence.
- rnavigate.plots.functions.functions.plot_interactions_arcs(ax, interactions, panel, yvalue=0, region='all')
Plot interactions as arcs.
Parameters
- axmatplotlib.axes.Axes
The axes to plot the interactions on.
- interactionsrnavigate.data.Interactions
The interactions to plot.
- panel“top” or “bottom”
The panel to plot the interactions on.
- yvaluefloat, optional
The y-value at which to plot the interactions.
- regiontuple of int, optional
The region of the sequence to plot interactions for.
- rnavigate.plots.functions.functions.plot_profile_bars(ax, profile, scale_factor=1, plot_error=True, bottom=0, region='all')
Plot per-nucleotide data as colored bars.
Parameters
- axmatplotlib.axes.Axes
The axes to plot the profile on.
- profilernavigate.data.Profile
The profile to plot.
- scale_factorfloat, optional
The factor by which to multiply per-nucleotide values.
- plot_errorbool, optional
Whether to plot error bars.
- bottomfloat, optional
The y-value at which to plot the bars.
- regiontuple of int, optional
The region of the sequence to plot bars for.
- rnavigate.plots.functions.functions.plot_profile_skyline(ax, profile, label, columns, errors)
Plot per-nucleotide data as a skyline plot.
Parameters
- axmatplotlib.axes.Axes
The axes to plot the profile on.
- profilernavigate.data.Profile
The profile to plot.
- labelstr
The label to use for the plot legend.
- columnslist of str
The columns of the profile to plot.
- errorslist of str
The columns of the profile to use for error bars.
- rnavigate.plots.functions.functions.plot_sequence_alignment(ax, alignment, labels, top=5, bottom=-5, ytrans='data')
Plot a sequence alignment.
Parameters
- axmatplotlib.axes.Axes
The axes to plot the alignment on.
- alignmentrnavigate.data.Alignment
The alignment to plot.
- labelstuple of str
The labels for the two sequences in the alignment.
- topint, optional
The y-value to plot the top sequence at.
- bottomint, optional
The y-value to plot the bottom sequence at.
- ytransstr, optional
The transform to use for the y-values. Valid options are “data” and “axes”.
- rnavigate.plots.functions.functions.set_nt_ticks(ax, sequence, region, major, minor)
Set the ticks and labels for a region of a sequence.
Dashes are ignored when counting nucleotide positions.
Parameters
- axmatplotlib.axes.Axes
The axes to set the ticks and labels of.
- sequencestr or rnavigate.data.Sequence
The sequence to set ticks and labels for.
- regiontuple of int
The region of the sequence to set ticks and labels for.
- majorint
The gap between major ticks.
- minorint
The gap between minor ticks.
rnavigate.plots.functions.ss module
- rnavigate.plots.functions.ss.plot_annotation_ss(ax, structure, annotation)
Highlight regions or nucleotides of interest on a secondary structure diagram.
Parameters
- axmatplotlib.axes.Axes
Axes to plot on.
- structurernavigate.data.SecondaryStructure
Secondary structure with diagram drawing coordinates.
- annotationrnavigate.data.Annotation
Annotation to plot.
- rnavigate.plots.functions.ss.plot_basepairs_ss(ax, structure, bp_style)
Plot the basepairs of a secondary structure diagram.
Parameters
- axmatplotlib.axes.Axes
Axes to plot on.
- structurernavigate.data.SecondaryStructure
Secondary structure with diagram drawing coordinates to plot.
- bp_style“conventional”, “dotted” or “line”
Style of basepairs to plot.
- rnavigate.plots.functions.ss.plot_interactions_ss(ax, structure, interactions)
Plot the interactions as lines over a secondary structure diagram.
Parameters
- axmatplotlib.axes.Axes
Axes to plot on.
- structurernavigate.data.SecondaryStructure
Secondary structure with diagram drawing coordinates.
- interactionsrnavigate.data.Interactions
Interactions to plot.
- rnavigate.plots.functions.ss.plot_nucleotides_ss(ax, structure, colors)
Plot the nucleotides of a secondary structure diagram.
Parameters
- axmatplotlib.axes.Axes
Axes to plot on.
- structurernavigate.data.SecondaryStructure
Secondary structure with diagram drawing coordinates to plot.
- colorslist
List of colors to use for each nucleotide in the structure.
- rnavigate.plots.functions.ss.plot_positions_ss(ax, structure, xticks=20)
Plot the positions of a secondary structure diagram.
Label locations are chosen from a point on a circle around each position that is the furthest from any other nucleotides. This sometimes causes tick marks and labels to overlap with other plot elements.
Parameters
- axmatplotlib.axes.Axes
Axes to plot on.
- structurernavigate.data.SecondaryStructure
Secondary structure with diagram drawing coordinates to plot.
- xticksint
Spacing between position labels.
- rnavigate.plots.functions.ss.plot_sequence_ss(ax, structure, colors)
Plot the sequence of a secondary structure diagram.
Parameters
- axmatplotlib.axes.Axes
Axes to plot on.
- structurernavigate.data.SecondaryStructure
Secondary structure with diagram drawing coordinates to plot.
- colorslist
List of colors to use for each nucleotide in the structure.
- rnavigate.plots.functions.ss.plot_structure_ss(ax, structure, colors)
Plot the structure of a secondary structure diagram.
Parameters
- axmatplotlib.axes.Axes
Axes to plot on.
- structurernavigate.data.SecondaryStructure
Secondary structure with diagram drawing coordinates to plot.
- colorslist
List of colors to use for each nucleotide in the structure.
rnavigate.plots.functions.tracks module
- rnavigate.plots.functions.tracks.plot_annotation_track(ax, annotation, yvalue, height, mode, region='all', ytrans='data')
Plot an annotation track along the x-axis of a plot.
Parameters
- axmatplotlib.axes.Axes
The axes to plot the annotation track on.
- annotationrnavigate.data.Annotation
The annotation to plot.
- yvaluefloat
The y-value of the annotation track.
- heightfloat
The height of the annotation track.
- mode“track” or “bar”
The annotation mode.
- regionlist of 2 int, defaults to “all”
Start and end positions of the region to plot. If “all”, plot the entire sequence.
- ytrans“data” or “axes”, defaults to “data”
The y-axis coordinate system.
- rnavigate.plots.functions.tracks.plot_domain_track(ax, spans, yvalue, height, region='all', ytrans='data')
Plot a domain track along the x-axis of a plot.
Parameters
- axmatplotlib.axes.Axes
The axes to plot the domain track on.
- spansrnavigate.data.Spans
The spans to plot.
- yvaluefloat
The y-value of the domain track.
- heightfloat
The height of the domain track.
- regionlist of 2 int, defaults to “all”
Start and end positions of the region to plot. If “all”, plot the entire sequence.
- ytrans“data” or “axes”, defaults to “data”
The y-axis coordinate system.
- rnavigate.plots.functions.tracks.plot_sequence_track(ax, sequence, yvalue=-0.05, height=0.05, ytrans='data', verticalalignment='bottom', region='all')
Plot a sequence track along the x-axis of a plot.
Parameters
- axmatplotlib.axes.Axes
The axes to plot the sequence track on.
- sequencestr
The sequence to plot.
- yvaluefloat, defaults to -0.05
The y-value of the sequence track.
- heightfloat, defaults to 0.05
The height of the sequence track.
- ytrans“data” or “axes”, defaults to “data”
The y-axis coordinate system.
- verticalalignment“top” or “bottom”, defaults to “bottom”
The vertical alignment of the sequence track.
- regionlist of 2 int, defaults to “all”
Start and end positions of the region to plot. If “all”, plot the entire sequence.
Module contents
- rnavigate.plots.functions.adjust_spines(ax, spines)
Places the given spines on the given axis, removes others.
Parameters
- axmatplotlib.axes.Axes
The axes to adjust the spines of.
- spineslist of str
The spines to adjust. Valid options are “left”, “right”, “top”, and “bottom”.
- rnavigate.plots.functions.box_xtick_labels(ax)
Place a transparent box behind the xtick labels of the provided axis.
- rnavigate.plots.functions.clip_spines(ax, spines)
Clips the given spines to the range of the ticks.
Parameters
- axmatplotlib.axes.Axes
The axes to clip the spines of.
- spineslist of str
The spines to clip. Valid options are “left”, “right”, “top”, and “bottom”.
- rnavigate.plots.functions.get_contrasting_colors(colors)
Get contrasting colors for a list of colors.
Returns a list of “k” (black) or “w” (white) for each color in the input list, which ever contrasts better with the input color.
Parameters
- colorslist of str
List of colors to get contrasting colors for.
Returns
- list of str
List of “k” or “w” for each color in the input list.
- rnavigate.plots.functions.get_nt_ticks(sequence, region, gap)
Get the ticks and labels for a region of a sequence.
Dashes are ignored when counting nucleotide positions.
Parameters
- sequencestr or rnavigate.data.Sequence
The sequence to get ticks and labels for.
- regiontuple of int
The region of the sequence to get ticks and labels for.
- gapint
The gap between major ticks.
Returns
- ticks, labelstuple of list of int
The ticks and labels for the given region of the sequence.
- rnavigate.plots.functions.plot_annotation_circle(ax, seq_circle, annotation, offset=1)
Plot annotations on a circle plot.
Parameters
- axmatplotlib.axes.Axes
The axes to plot on.
- seq_circlernavigate.data.SequenceCircle
The sequence circle object containing nucleotide positions.
- annotationrnavigate.data.Annotation
The annotation to be plotted.
- offsetfloat, optional
The offset from the circle circumference to plot the annotation.
- rnavigate.plots.functions.plot_annotation_ss(ax, structure, annotation)
Highlight regions or nucleotides of interest on a secondary structure diagram.
Parameters
- axmatplotlib.axes.Axes
Axes to plot on.
- structurernavigate.data.SecondaryStructure
Secondary structure with diagram drawing coordinates.
- annotationrnavigate.data.Annotation
Annotation to plot.
- rnavigate.plots.functions.plot_annotation_track(ax, annotation, yvalue, height, mode, region='all', ytrans='data')
Plot an annotation track along the x-axis of a plot.
Parameters
- axmatplotlib.axes.Axes
The axes to plot the annotation track on.
- annotationrnavigate.data.Annotation
The annotation to plot.
- yvaluefloat
The y-value of the annotation track.
- heightfloat
The height of the annotation track.
- mode“track” or “bar”
The annotation mode.
- regionlist of 2 int, defaults to “all”
Start and end positions of the region to plot. If “all”, plot the entire sequence.
- ytrans“data” or “axes”, defaults to “data”
The y-axis coordinate system.
- rnavigate.plots.functions.plot_basepairs_ss(ax, structure, bp_style)
Plot the basepairs of a secondary structure diagram.
Parameters
- axmatplotlib.axes.Axes
Axes to plot on.
- structurernavigate.data.SecondaryStructure
Secondary structure with diagram drawing coordinates to plot.
- bp_style“conventional”, “dotted” or “line”
Style of basepairs to plot.
- rnavigate.plots.functions.plot_domain_track(ax, spans, yvalue, height, region='all', ytrans='data')
Plot a domain track along the x-axis of a plot.
Parameters
- axmatplotlib.axes.Axes
The axes to plot the domain track on.
- spansrnavigate.data.Spans
The spans to plot.
- yvaluefloat
The y-value of the domain track.
- heightfloat
The height of the domain track.
- regionlist of 2 int, defaults to “all”
Start and end positions of the region to plot. If “all”, plot the entire sequence.
- ytrans“data” or “axes”, defaults to “data”
The y-axis coordinate system.
- rnavigate.plots.functions.plot_interactions_arcs(ax, interactions, panel, yvalue=0, region='all')
Plot interactions as arcs.
Parameters
- axmatplotlib.axes.Axes
The axes to plot the interactions on.
- interactionsrnavigate.data.Interactions
The interactions to plot.
- panel“top” or “bottom”
The panel to plot the interactions on.
- yvaluefloat, optional
The y-value at which to plot the interactions.
- regiontuple of int, optional
The region of the sequence to plot interactions for.
- rnavigate.plots.functions.plot_interactions_circle(ax, seq_circle, interactions)
Plot interactions on a circle plot.
Parameters
- axmatplotlib.axes.Axes
The axes to plot on.
- seq_circlernavigate.data.SequenceCircle
The sequence circle object containing nucleotide positions.
- interactionsrnavigate.data.Interactions
The interactions to be plotted as arcs between nucleotides.
- rnavigate.plots.functions.plot_interactions_ss(ax, structure, interactions)
Plot the interactions as lines over a secondary structure diagram.
Parameters
- axmatplotlib.axes.Axes
Axes to plot on.
- structurernavigate.data.SecondaryStructure
Secondary structure with diagram drawing coordinates.
- interactionsrnavigate.data.Interactions
Interactions to plot.
- rnavigate.plots.functions.plot_nucleotides_ss(ax, structure, colors)
Plot the nucleotides of a secondary structure diagram.
Parameters
- axmatplotlib.axes.Axes
Axes to plot on.
- structurernavigate.data.SecondaryStructure
Secondary structure with diagram drawing coordinates to plot.
- colorslist
List of colors to use for each nucleotide in the structure.
- rnavigate.plots.functions.plot_positions_ss(ax, structure, xticks=20)
Plot the positions of a secondary structure diagram.
Label locations are chosen from a point on a circle around each position that is the furthest from any other nucleotides. This sometimes causes tick marks and labels to overlap with other plot elements.
Parameters
- axmatplotlib.axes.Axes
Axes to plot on.
- structurernavigate.data.SecondaryStructure
Secondary structure with diagram drawing coordinates to plot.
- xticksint
Spacing between position labels.
- rnavigate.plots.functions.plot_profile_bars(ax, profile, scale_factor=1, plot_error=True, bottom=0, region='all')
Plot per-nucleotide data as colored bars.
Parameters
- axmatplotlib.axes.Axes
The axes to plot the profile on.
- profilernavigate.data.Profile
The profile to plot.
- scale_factorfloat, optional
The factor by which to multiply per-nucleotide values.
- plot_errorbool, optional
Whether to plot error bars.
- bottomfloat, optional
The y-value at which to plot the bars.
- regiontuple of int, optional
The region of the sequence to plot bars for.
- rnavigate.plots.functions.plot_profile_skyline(ax, profile, label, columns, errors)
Plot per-nucleotide data as a skyline plot.
Parameters
- axmatplotlib.axes.Axes
The axes to plot the profile on.
- profilernavigate.data.Profile
The profile to plot.
- labelstr
The label to use for the plot legend.
- columnslist of str
The columns of the profile to plot.
- errorslist of str
The columns of the profile to use for error bars.
- rnavigate.plots.functions.plot_sequence_alignment(ax, alignment, labels, top=5, bottom=-5, ytrans='data')
Plot a sequence alignment.
Parameters
- axmatplotlib.axes.Axes
The axes to plot the alignment on.
- alignmentrnavigate.data.Alignment
The alignment to plot.
- labelstuple of str
The labels for the two sequences in the alignment.
- topint, optional
The y-value to plot the top sequence at.
- bottomint, optional
The y-value to plot the bottom sequence at.
- ytransstr, optional
The transform to use for the y-values. Valid options are “data” and “axes”.
- rnavigate.plots.functions.plot_sequence_ss(ax, structure, colors)
Plot the sequence of a secondary structure diagram.
Parameters
- axmatplotlib.axes.Axes
Axes to plot on.
- structurernavigate.data.SecondaryStructure
Secondary structure with diagram drawing coordinates to plot.
- colorslist
List of colors to use for each nucleotide in the structure.
- rnavigate.plots.functions.plot_sequence_track(ax, sequence, yvalue=-0.05, height=0.05, ytrans='data', verticalalignment='bottom', region='all')
Plot a sequence track along the x-axis of a plot.
Parameters
- axmatplotlib.axes.Axes
The axes to plot the sequence track on.
- sequencestr
The sequence to plot.
- yvaluefloat, defaults to -0.05
The y-value of the sequence track.
- heightfloat, defaults to 0.05
The height of the sequence track.
- ytrans“data” or “axes”, defaults to “data”
The y-axis coordinate system.
- verticalalignment“top” or “bottom”, defaults to “bottom”
The vertical alignment of the sequence track.
- regionlist of 2 int, defaults to “all”
Start and end positions of the region to plot. If “all”, plot the entire sequence.
- rnavigate.plots.functions.plot_structure_ss(ax, structure, colors)
Plot the structure of a secondary structure diagram.
Parameters
- axmatplotlib.axes.Axes
Axes to plot on.
- structurernavigate.data.SecondaryStructure
Secondary structure with diagram drawing coordinates to plot.
- colorslist
List of colors to use for each nucleotide in the structure.
- rnavigate.plots.functions.set_nt_ticks(ax, sequence, region, major, minor)
Set the ticks and labels for a region of a sequence.
Dashes are ignored when counting nucleotide positions.
Parameters
- axmatplotlib.axes.Axes
The axes to set the ticks and labels of.
- sequencestr or rnavigate.data.Sequence
The sequence to set ticks and labels for.
- regiontuple of int
The region of the sequence to set ticks and labels for.
- majorint
The gap between major ticks.
- minorint
The gap between minor ticks.