rstoolbox.plot.sequence_frequency_plot¶

rstoolbox.plot.sequence_frequency_plot(df, seqID, ax, aminosY=True, clean_unused=-1, refseq=True, key_residues=None, border_color='green', border_width=2, labelsize=None, xrotation=0, yrotation=0, **kwargs)¶

Makes a heatmap subplot into the provided axis showing the sequence distribution of each residue type for each position.

A part from the function arguments, any argument that can be provided to the seaborn.heatmap() function can also be provided here.

By default, the heatmap generated will have the residue types as y-axis and the sequence positions as x-axis.

Some tips:

1. Do you want to set the orientation of the color bar vertical? Add the parameter: cbar_kws={"orientation": "vertical"}
2. Do you want to put the color bar in a different axis? This is quite recommendable, as the color bar in the same axis does not tend to look that good. Add the parameter: cbar_ax=[second_axis]
3. You don’t want a color bar? Add the parameter: cbar=False

Parameters:

df (Union[DesignFrame, SequenceFrame]) – Data container. seqID (str) – Identifier of the sequence of interest. ax (Axes) – Where to plot the heatmap. aminosY (bool) – Set to False to get invert the orientation of the heatmap. clean_unused (float) – Remove amino acids from the plot when they never get represented over the given frequency. Residues present in the reference sequence are not taken into account. refseq (rbool) – if True (default), mark the original residues according to the reference sequence. key_residues (Union[int, list() of int, str, Selection]) – Residues of interest. border_color (Union[int, str]) – Color to use to mark the original residue types. border_width (int) – Line width used to mark the original residue types. labelsize (int) – Change the size of the text in the axis. xrotation (float) – Rotation to apply in the x-axis text (degrees). yrotation (float) – Rotation to apply in the y-axis text (degrees).

Note

Attribute clean_unused, if applied deletes the full column/row assigned to an unrepresented residue type, this means that if that residue type is part of the refseq, it will not be labeled.

Raises:	ValueError: if input is not a DataFrame derived object. KeyError: if there is no reference_sequence for chain seqID of the decoys.

Example

In [1]: from rstoolbox.io import parse_rosetta_file
   ...: from rstoolbox.plot import sequence_frequency_plot
   ...: import matplotlib.pyplot as plt
   ...: df = parse_rosetta_file("../rstoolbox/tests/data/input_2seq.minisilent.gz",
   ...:                         {"sequence": "B"})
   ...: fig = plt.figure(figsize=(25, 10))
   ...: ax = plt.subplot2grid((1, 1), (0, 0))
   ...: sequence_frequency_plot(df, "B", ax, refseq=False, cbar=False, xrotation=90)
   ...: 

In [2]: plt.show()

In [3]: plt.close()