mgkit.plots.unused module¶
New in version 0.1.14.
Code deprecated or untested
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mgkit.plots.unused.
barchart_categories
(data, colours=None, title='', tickfont='small', xlabel_dict=None, barlabel_dict=None, width=0.9, rotation='vertical', file_name=None, fig_size=None, fig_aspect=None)¶ Parameters: - data – DataFrame where the number of rows indicates how many bars will plotted per column
- colours – must be equal the number of data rows if supplied or it will be blue by default
- title – chart title
- tickfont – font size for ticks (only for column axis)
- xlabel_dict – a mapping to the acual labels to use for the columns. Defaults to columns’ names
- barlabel_dict – a mapping to the acual labels to use for the row. Defaults to rows’ names
- width – bar width
Returns: axis instance
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mgkit.plots.unused.
get_taxon_colors_new
(taxa, taxonomy, default_colour='#ffff33')¶ Returns a dictionary of taxa and their assigned colours based on
TAXON_COLOURS
and the taxonomy provided. Uses thetaxon.UniprotTaxonomy.get_taxon_root()
to determine the root of a taxon.Parameters: - taxa (iterable) – iterable of taxon ids
- taxonomy (UniprotTaxonomy) – taxonomy instance
- default_colour – colour used in case there’s no known root for the taxon
Return dict: dictionary mapping taxon_id to colour
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mgkit.plots.unused.
lineplot_values_on_second_axis
(*args, **kwargs)¶ Deprecated since version 0.1.13.
Adds a lineplot on a second axis using twinx
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mgkit.plots.unused.
map_taxon_to_colours
(taxa, taxonomy, default_colour='#ffff33')¶ Returns a dictionary of taxa and their assigned colours based on
TAXON_COLOURS
and the taxonomy provided. Uses thetaxon.UniprotTaxonomy.get_taxon_root()
to determine the root of a taxon.Parameters: - taxa (iterable) – iterable of taxon ids
- taxonomy (UniprotTaxonomy) – taxonomy instance
- default_colour – colour used in case there’s no known root for the taxon
Return dict: dictionary mapping taxon_id to colour
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mgkit.plots.unused.
plot_contig_assignment_bar
(series, taxon_colours=None, log_scale=False, index=None, file_name=None, fig_aspect=None, xlabels_size=8)¶ Plots barchart for contig assignment
Parameters: - series –
pandas.Series
instance with the data - taxon_colours (dict) – colour of the bars for each taxon
- log_scale (bool) – if True the y axis is log scaled
- fig_aspect (tuple) – tuple with figure size
- xlabels_size (int) – size of the taxon labels
- index – optional
pandas.Index
used to reindex the series - file_name (str) – name of the file to write the graph to
- series –
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mgkit.plots.unused.
plot_scatter_2d
(data, labels, colours=None, pointsize=10.0, title='', xlabel='', ylabel='', centers=None, marker='*', marker_colour=None, markersize=None, hull_points=True, linewidth=0.2, legend=True, anno_center=True)¶ Scatter plot in 2d. Used for cluster results
Parameters: - data (array) –
numpy.array
with shape n, 2 - labels (array) – labels to categorise samples
- colours (dict) – dictionary whose keys are the labels and the values
are valid
matplotlib
colours - pointsize (int) – point size
- title (str) – plot title
- xlabel (str) – label for x axis
- ylabel (str) – label for y axis
Returns: axis instance
- data (array) –
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mgkit.plots.unused.
plot_scatter_3d
(data, labels, colours=None, pointsize=10.0, title='', xlabel='', ylabel='', zlabel='')¶ Scatter plot in 3d. Used for cluster results
Parameters: - data (array) –
numpy.array
with shape n, 3 - labels (array) – labels to categorise samples
- colours (dict) – dictionary whose keys are the labels and the values
are valid
matplotlib
colours - pointsize (int) – point size
- title (str) – plot title
- xlabel (str) – label for x axis
- ylabel (str) – label for y axis
- zlabel (str) – label for z axis
Returns: axis instance
- data (array) –
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mgkit.plots.unused.
scatter_gene_values
(gene_dict, xlabel='Profile pN/pS', ylabel='Rumen pN/pS', title='', colours=None, file_name=None, plot_order=None, line_colour='r', max_limit=None, axes=None)¶ Plots gene-taxon pN/pS from profiles against their observed values.
Parameters: - gene_dict (dict) – dictionary that contains the data
- xlabel (str) – label for x axis
- ylabel (str) – label for y axis
- title (str) – graph title
- colours – colours used in for the different datasets; defaults to TAXON_COLOURS
- file_name (str) – path to which the graph is to be saved (by default) it doesn’t write to disk
- plot_order (iterable) – the order used in plotting the data points; default to the order of the gene_dict dictionary keys
- coloUr – valid colour for the lines in the plot
- max_limit (float) – used to put a limit on the plot
- axes – optional axes used to draw the scatter plot
Returns: the axis object used for the plot