pyamr.graphics package

Submodules

pyamr.graphics.antibiogram module

Classes:

Antibiogram([column_organism, ...])

class pyamr.graphics.antibiogram.Antibiogram(column_organism='SPECIE', column_antibiotic='ANTIBIOTIC', column_genus='GENUS', column_category='CATEGORY', column_index='SARI', colormap_genus='nipy_spectral', colormap_category='tab20b', discard_intrinsic=False)

Bases: object

Attributes:

c_abx
c_cat
c_gen
c_idx
c_org

Methods:

fit(dataframe)	This method fits the antibiogram to the data.
plot([organisms, antibiotics, genera, ...])	This function plots the antibiogram.

c_abx = 'ANTIBIOTIC'

c_cat = 'CATEGORY'

c_gen = 'GENUS'

c_idx = 'SARI'

c_org = 'SPECIE'

fit(dataframe)

This method fits the antibiogram to the data.

Parameters:

dataframe (pd.DataFrame) – The…

Return type:

Antibiogram instance

plot(organisms=None, antibiotics=None, genera=None, categories=None, method='weighted', metric='euclidean', vmin=0.0, vmax=1.0, cmap=None, figsize=(5, 5), xticklabels=True, yticklabels=True, **kwargs)

This function plots the antibiogram.

The arguments are those to be passed to the clustermap implementation which is available on seaborn.

Parameters:

• method (string-like)

• metric (string-like)

• vmin, vmax (float-like, float-like) – The min and maximum values within the matrix (or feasible range).

• cmap (string-like) – The colormap to be used to plot the resistance indexes.

• figsize (tuple-like) – The size of the figure

Return type:

an axis object

pyamr.graphics.table_graph module

Classes:

TableGraph()
TableGraph2()

class pyamr.graphics.table_graph.TableGraph

Bases: object

Attributes:

fontsize

Methods:

get_map_config([title, xlim, xsym, xticks, ...])	This function helps creating a configuration map.
plot(data, **kwargs)
plot_array(x[, ax, ax_kwargs, cmap_kwargs, ...])	this method plots a single column.
plot_dataframe(dataframe[, axes, configuration])	This method plots the whole table.
plot_matrix(data[, axes, ylabels, clabels, ...])	This method plots a matrix.
plot_vertical_line(ax, top, xv[, bg, lw, cb])	This function adds a vertical line and background

fontsize = 9

get_map_config(title=None, xlim=None, xsym=False, xticks=None, xline=[], vmin=None, vmax=None, vsym=False, cmap='Blues', midpoint=None, s=80, linewidths=0.75, edgecolor='gray', **kwargs)

This function helps creating a configuration map.

plot(data, **kwargs)

plot_array(x, ax=None, ax_kwargs={}, cmap_kwargs={}, scatter_kwargs={}, **kwargs)

this method plots a single column.

Parameters:

• x (values to plot.)

• ax (axis to plot the information.)

• ax_kwargs (axis configuration information.)

• cmap_kwargs (cmap configuration information.)

• scatter_kwargs (scatter configuration information.)

Returns:

axis

Return type:

the axis in which the series is plotted.

plot_dataframe(dataframe, axes=None, configuration={})

This method plots the whole table.

Parameters:

• dataframe

• configuration

plot_matrix(data, axes=None, ylabels=None, clabels=None, configuration={})

This method plots a matrix.

Parameters:

• data

• ylabels

• configuration

plot_vertical_line(ax, top, xv, bg=None, lw=1.0, cb=None)

This function adds a vertical line and background

Parameters:

• ax (the axis to plot the line.)

• top (the height of the vertical line.)

• xv (the x value where the line should be placed.)

• bg (the x value where the background should be extended.)

class pyamr.graphics.table_graph.TableGraph2

Bases: object

Methods:

add_vline(ax, top, xv[, bg])	This function adds a vertical line and background
check_vmin_vmax(x, kwargs)	This methos check the vmax and vmin for colors.
display_column(x, y, cmap, ax, **kwargs)	This method displays a single column.
plot(df, axes, information)	This method plots the whole table.

add_vline(ax, top, xv, bg=None)

This function adds a vertical line and background

check_vmin_vmax(x, kwargs)

This methos check the vmax and vmin for colors.

display_column(x, y, cmap, ax, **kwargs)

This method displays a single column.

plot(df, axes, information)

This method plots the whole table.

pyamr.graphics.utils_to_delete module

Classes:

MidpointNormalize([vmin, vmax, midpoint, clip])

Normalise the colorbar so that diverging bars

Functions:

hlinebgplot(ax, right, yv[, bg])	This function adds a vertical line and background
scalar_colormap(values, cmap, vmin, vmax)	This method creates a colormap based on values.
vlinebgplot(ax, top, xv[, bg])	This function adds a vertical line and background

class pyamr.graphics.utils_to_delete.MidpointNormalize(vmin=None, vmax=None, midpoint=None, clip=False)

Bases: Normalize

Normalise the colorbar so that diverging bars

work there way either side from a prescribed midpoint value)

Example

> MidpointNormalize(midpoint=0., vmin=-100, vmax=100)

pyamr.graphics.utils_to_delete.hlinebgplot(ax, right, yv, bg=None)

This function adds a vertical line and background

pyamr.graphics.utils_to_delete.scalar_colormap(values, cmap, vmin, vmax)

This method creates a colormap based on values.

Parameters:

• values (array-like) – The values to create the corresponding colors

• cmap (str) – The colormap

• vmin, vmax (float) – The minimum and maximum possible values

Return type:

scalar colormap

pyamr.graphics.utils_to_delete.vlinebgplot(ax, top, xv, bg=None)

This function adds a vertical line and background

Parameters:

• ax (matplotlib axes)

• top (float) – The max y value

• xv (float) – The x value

• bg (boolean) – Whether to include a background

Module contents