Axial

For more information about the scientific uses of Axial, please see the Readme. To report an issue, please refer to the Issues.

axial.volcano(differential_dfs, title='Axial Volcano Plot', scripts_mode='CDN', data_mode='directory', organism='human', q_value_column_name='q', log2FC_column_name='logFC', output_dir='.', filename='volcano.html', version='0.2.2')

Parameters:

• differential_dfs (dict or pandas.DataFrame) – python dict of names to pandas dataframes, or a single dataframe, indexed by gene symbols which must have columns named log2FC and qval.
• title (str) – The title of the plot (to be embedded in the html).
• scripts_mode (str) –

  Choose from [“CDN”, “directory”, “inline”]:

  • ”CDN” compiles a single HTML page with links to scripts hosted on a CDN,
  • ”directory” compiles a directory with all scripts locally cached,
  • ”inline” compiles a single HTML file with all scripts/styles inlined.
• data_mode (str) –

  Choose from [“directory”, “inline”]:

  • ”directory” compiles a directory with all data locally cached,
  • ”inline” compiles a single HTML file with all data inlined.
• organism (str) – “human” or “mouse”
• q_value_column_name (str) –
• log2FC_column_name (str) –
• output_dir (str) – the directory in which to output the file
• filename (str) – the filename of the output file
• version (str) – the version of the javascripts to use. Leave the default to pin the version, or choose “latest” to get updates, or choose part of the version string to get minor updates.

Returns:

The filepath which the html was outputted to.

Return type:

Path

axial.bar(differential_dfs, title='Axial Pathway Bar Plot', scripts_mode='CDN', data_mode='directory', organism='human', q_value_column_name='q', log2FC_column_name='logFC', output_dir='.', filename='bar.html', version='0.2.2')

Parameters:

• differential_dfs (dict or pandas.DataFrame) – python dict of names to pandas dataframes, or a single dataframe, indexed by gene symbols which must have columns named log2FC and qval.
• title (str) – The title of the plot (to be embedded in the html).
• scripts_mode (str) –

  Choose from [“CDN”, “directory”, “inline”]:

  • ”CDN” compiles a single HTML page with links to scripts hosted on a CDN,
  • ”directory” compiles a directory with all scripts locally cached,
  • ”inline” compiles a single HTML file with all scripts/styles inlined.
• data_mode (str) –

  Choose from [“directory”, “inline”]:

  • ”directory” compiles a directory with all data locally cached,
  • ”inline” compiles a single HTML file with all data inlined.
• organism (str) – “human” or “mouse”
• q_value_column_name (str) –
• log2FC_column_name (str) –
• output_dir (str) – the directory in which to output the file
• filename (str) – the filename of the output file
• version (str) – the version of the javascripts to use. Leave the default to pin the version, or choose “latest” to get updates, or choose part of the version string to get minor updates.

Returns:

The filepath which the html was outputted to.

Return type:

Path

axial.braid(genes_by_samples_matrix, sample_attributes, title='Axial Braid Plot', scripts_mode='CDN', data_mode='directory', organism='human', output_dir='.', filename='braid.html', version='0.2.2')

Parameters:

• genes_by_samples_matrix (pandas.DataFrame) – dataframe indexed by genes, columns are samples
• sample_attributes (pandas.DataFrame) – dataframe indexed by samples, columns are sample attributes (e.g. classes)
• title (str) – The title of the plot (to be embedded in the html).
• scripts_mode (str) –

  Choose from [“CDN”, “directory”, “inline”]:

  • ”CDN” compiles a single HTML page with links to scripts hosted on a CDN,
  • ”directory” compiles a directory with all scripts locally cached,
  • ”inline” compiles a single HTML file with all scripts/styles inlined.
• data_mode (str) –

  Choose from [“directory”, “inline”]:

  • ”directory” compiles a directory with all data locally cached,
  • ”inline” compiles a single HTML file with all data inlined.
• organism (str) – “human” or “mouse”
• output_dir (str) – the directory in which to output the file
• filename (str) – the filename of the output file
• version (str) – the version of the javascripts to use. Leave the default to pin the version, or choose “latest” to get updates, or choose part of the version string to get minor updates.

Returns:

The filepath which the html was outputted to.

Return type:

Path

axial.heatmap(genes_by_samples_matrix, sample_attributes, title='Axial Heatmap', scripts_mode='CDN', data_mode='directory', organism='human', separate_zscore_by=['system'], output_dir='.', filename='heatmap.html', version='0.2.2')

Parameters:

• genes_by_samples_matrix (pandas.DataFrame) – dataframe indexed by genes, columns are samples
• sample_attributes (pandas.DataFrame) – dataframe indexed by samples, columns are sample attributes (e.g. classes)
• title (str) – The title of the plot (to be embedded in the html).
• scripts_mode (str) –

  Choose from [“CDN”, “directory”, “inline”]:

  • ”CDN” compiles a single HTML page with links to scripts hosted on a CDN,
  • ”directory” compiles a directory with all scripts locally cached,
  • ”inline” compiles a single HTML file with all scripts/styles inlined.
• data_mode (str) –

  Choose from [“directory”, “inline”]:

  • ”directory” compiles a directory with all data locally cached,
  • ”inline” compiles a single HTML file with all data inlined.
• organism (str) – “human” or “mouse”
• separate_zscore_by (list) –
• output_dir (str) – the directory in which to output the file
• filename (str) – the filename of the output file
• version (str) – the version of the javascripts to use. Leave the default to pin the version, or choose “latest” to get updates, or choose part of the version string to get minor updates.

Returns:

The filepath which the html was outputted to.

Return type:

Path

axial.graph(networkx_graph, title='Axial Graph Visualization', scripts_mode='CDN', data_mode='directory', output_dir='.', filename='graph.html', version='0.2.2')

Parameters:

• networkx_graph (networkx.Graph) – any instance of networkx.Graph
• title (str) – The title of the plot (to be embedded in the html).
• scripts_mode (str) –

  Choose from [“CDN”, “directory”, “inline”]:

  • ”CDN” compiles a single HTML page with links to scripts hosted on a CDN,
  • ”directory” compiles a directory with all scripts locally cached,
  • ”inline” compiles a single HTML file with all scripts/styles inlined.
• data_mode (str) –

  Choose from [“directory”, “inline”]:

  • ”directory” compiles a directory with all data locally cached,
  • ”inline” compiles a single HTML file with all data inlined.
• output_dir (str) – the directory in which to output the file
• filename (str) – the filename of the output file
• version (str) – the version of the javascripts to use. Leave the default to pin the version, or choose “latest” to get updates, or choose part of the version string to get minor updates.

Returns:

The filepath which the html was outputted to.

Return type:

Path