`pymodulon.imodulondb`

Functions for writing a directory for iModulonDB webpages

Module Contents

Functions

`imodulondb_compatibility`(model, inplace=False, tfcomplex_to_gene=None)	Checks for all issues and missing information prior to exporting to iModulonDB.
`imodulondb_export`(model, path='.', cat_order=None, tfcomplex_to_gene=None, skip_iMs=False, skip_genes=False)	Generates the iModulonDB page for the data and exports to the path.
`imdb_dataset_table`(model)	Converts the model’s imodulondb_table into dataset metadata
`imdb_iM_table`(imodulon_table, cat_order=None)	Reformats the iModulon table according
`imdb_gene_presence`(model)	Generates the two versions of the gene presence file, one as a binary
`imodulondb_main_site_files`(model, path_prefix='.', rewrite_annotations=True, cat_order=None)	Generates all parts of the site that do not require large iteration loops
`imdb_generate_im_files`(model, path_prefix='.', gene_scatter_x='start', tfcomplex_to_gene=None)	Generates all files for all iModulons in data
`imdb_generate_gene_files`(model, path_prefix='.')	Generates all files for all iModulons in IcaData object
`parse_tf_string`(model, tf_str, verbose=False)	Returns a list of relevant tfs from a string. Will ignore TFs not in the
`imdb_gene_table_df`(model, k)	Creates the gene table dataframe for iModulonDB
`_component_DF`(model, k, tfs=None)	Helper function for imdb_gene_hist_df
`_tf_combo_string`(row)	Creates a formatted string for the histogram legends. Helper function for
`_sort_tf_strings`(tfs, unique_elts)	Sorts TF strings for the legend of the histogram. Helper function for
`imdb_gene_hist_df`(model, k, bins=20, tol=0.001)	Creates the gene histogram for an iModulon
`_gene_color_dict`(model)	Helper function to match genes to colors based on COG. Used by
`imdb_gene_scatter_df`(model, k, gene_scatter_x='start')	Generates a dataframe for the gene scatter plot in iModulonDB
`generate_n_replicates_column`(model)	Generates the “n_replicates” column of the sample_table for iModulonDB.
`imdb_activity_bar_df`(model, k)	Generates a dataframe for the activity bar graph of iModulon k
`_parse_regulon_string`(model, s)	The Bacillus microarray dataset uses [] to create unusually complicated
`_get_reg_genes`(model, tf)	Finds the set of genes regulated by the boolean combination of regulators
`imdb_regulon_venn_df`(model, k)	Generates a dataframe for the regulon venn diagram of iModulon k. Returns
`get_tfs_to_scatter`(model, tf_string, tfcomplex_to_genename=None, verbose=False)	param model IcaData object
`imdb_regulon_scatter_df`(model, k, tfcomplex_to_genename=None)	param model IcaData object
`tf_with_links`(model, tf_str)	Adds links to the regulator string
`tf_with_links_brackets`(model, tf_str)	Adds links to the regulator string
`imdb_imodulon_basics_df`(model, k, reg_venn, reg_scatter)	Generates a dataframe for the metadata of iModulon k
`make_im_directory`(model, k, path_prefix='.', gene_scatter_x='start', tfcomplex_to_genename=None)	param model IcaData object
`imdb_gene_activity_bar_df`(model, gene_id)	param model IcaData object
`imdb_gene_im_table_df`(model, g, im_table, m_bin)	Generates a dataframe for the iModulon table of gene g
`imdb_gene_basics_df`(model, g)	param model IcaData object
`make_gene_directory`(model, g, path_prefix='.')	Generates all data for gene g, stores it in a subfolder of path_prefix

pymodulon.imodulondb.imodulondb_compatibility(model, inplace=False, tfcomplex_to_gene=None)[source]

Checks for all issues and missing information prior to exporting to iModulonDB. If inplace = True, modifies the model (not recommended for main model variables).

Parameters

model (IcaData) – IcaData object to check
inplace (bool, optional) – If true, modifies the model to prepare for export. Not recommended for use with your main model variable.
tfcomplex_to_gene (dict, optional) – dictionary pointing complex TRN entries to matching gene names in the gene table (ex: {“FlhDC”:”flhD”})

Returns

table_issues (pd.DataFrame) – Each row corresponds to an issue with one of the main class elements. Columns: * Table: which table or other variable the issue is in * Missing Column: the column of the Table with the issue (not case sensitive; capitalization is ignored). * Solution: Unless “CRITICAL” is in this cell, the site behavior if the issue remained is described here.
tf_issues (pd.DataFrame) – Each row corresponds to a regulator that is used in the imodulon_table. Columns: * in_trn: whether the regulator is in the model.trn. Regulators not in the TRN will be ignored in the site’s histograms and gene tables. * has_link: whether the regulator has a link in tf_links. If not, no link to external regulator databases will be shown. * has_gene: whether the regulator can be matched to a gene in the model. If this is false, then there will be no regulator scatter plot on the site. You can link TF complexes to one of their genes using the tfcomplex_to_gene input.
missing_g_links (pd.Series) – The genes on this list don’t have links in the gene_links. Their gene pages for these genes will not display links.
missing_DOIs (pd.Series) – The samples listed here don’t have DOIs in the sample_table. Clicking on their associated bars in the activity plots will not link to relevant papers.

pymodulon.imodulondb.imodulondb_export(model, path='.', cat_order=None, tfcomplex_to_gene=None, skip_iMs=False, skip_genes=False)[source]

Generates the iModulonDB page for the data and exports to the path. If certain columns are unavailable but can be filled in automatically, they will be.

Parameters

model (IcaData) – IcaData object to export
path (str, optional) – Path to iModulonDB main hosting folder (default = “.”)
cat_order (list, optional) – List of categories in the imodulon_table, ordered as you would like them to appear in the dataset table (default = None)
tfcomplex_to_gene (dict, optional) – dictionary pointing complex TRN entries to matching gene names in the gene table ex: {“FlhDC”:”flhD”}
skip_iMs (bool, optional) – If this is True, do not output iModulon files (to save time)
skip_genes (bool, optional) – If this is True, do not output gene files (to save time)

Returns

None

Return type

None

pymodulon.imodulondb.imdb_dataset_table(model)[source]

Converts the model’s imodulondb_table into dataset metadata for the gray box on the left side of the dataset page

Parameters: model (IcaData) – An IcaData object
Returns: res – A series of formatted metadata
Return type: Series

pymodulon.imodulondb.imdb_iM_table(imodulon_table, cat_order=None)[source]

Reformats the iModulon table according

Parameters

imodulon_table (DataFrame) – Table formatted similar to IcaData.imodulon_table
cat_order (list, optional) – List of categories in imodulon_table.category, ordered as desired

Returns

im_table – New iModulon table with the columns expected by iModulonDB

Return type

DataFrame

pymodulon.imodulondb.imdb_gene_presence(model)[source]

Generates the two versions of the gene presence file, one as a binary matrix, and one as a DataFrame

Parameters

model (IcaData) – An IcaData object

Returns

mbin (~pandas.DataFrame) – Binarized M matrix
mbin_list (~pandas.DataFrame) – Table mapping genes to iModulons

pymodulon.imodulondb.imodulondb_main_site_files(model, path_prefix='.', rewrite_annotations=True, cat_order=None)[source]

Generates all parts of the site that do not require large iteration loops

Parameters

model (IcaData) – IcaData object
path_prefix (str, optional) – Main folder for iModulonDB files (default = “.”)
rewrite_annotations (bool, optional) – Set to False if the gene_table and trn are unchanged (default = True)
cat_order (list, optional) – list of categories in data.imodulon_table.category, ordered as you want them to appear on the dataset page (default = None)

Returns

main_folder – Dataset folder, for use as the path_prefix in imdb_generate_im_files()

Return type

str

pymodulon.imodulondb.imdb_generate_im_files(model, path_prefix='.', gene_scatter_x='start', tfcomplex_to_gene=None)[source]

Generates all files for all iModulons in data

Parameters

model (IcaData) – IcaData object
path_prefix (str, optional) – Dataset folder in which to store the files (default = “.”)
gene_scatter_x (str) – Column from the gene table that specificies what to use on the X-axis of the gene scatter plot (default = “start”)
tfcomplex_to_gene (dict, optional) – dictionary pointing complex TRN entries to matching gene names in the gene table ex: {“FlhDC”:”flhD”}

pymodulon.imodulondb.imdb_generate_gene_files(model, path_prefix='.')[source]

Generates all files for all iModulons in IcaData object

Parameters

model (IcaData) – IcaData object
path_prefix (str, optional) – Dataset folder in which to store the files (default = “.”)

Returns

Return type

None

pymodulon.imodulondb.parse_tf_string(model, tf_str, verbose=False)[source]

Returns a list of relevant tfs from a string. Will ignore TFs not in the trn file. iModulonDB helper function.

Parameters

model (IcaData) – IcaData object
tf_str (str) – String of tfs joined by ‘+’ and ‘/’ operators
verbose (bool, optional) – Whether or nor to print outputs

Returns

tfs – List of relevant TFs

Return type

list

pymodulon.imodulondb.imdb_gene_table_df(model, k)[source]

Creates the gene table dataframe for iModulonDB :param model: IcaData object :type model: IcaData :param k: iModulon name :type k: int or str

Returns: res – DataFrame of the gene table that is compatible with iModulonDB
Return type: DataFrame

pymodulon.imodulondb._component_DF(model, k, tfs=None)[source]

Helper function for imdb_gene_hist_df

Parameters

model (IcaData) – IcaData object
k (int or str) – iModulon name
tfs (list) – List of TFs (default = None)

Returns

gene_table – Gene table for the iModulon

Return type

DataFrame

pymodulon.imodulondb._tf_combo_string(row)[source]

Creates a formatted string for the histogram legends. Helper function for imdb_gene_hist_df.

Parameters: row (Series) – Boolean series indexed by TFs for a given gene
Returns: A string formatted for display (i.e. “Regulated by …”)
Return type: str

pymodulon.imodulondb._sort_tf_strings(tfs, unique_elts)[source]

Sorts TF strings for the legend of the histogram. Helper function for imdb_gene_hist_df.

Parameters

tfs (list[str]) – Sequence of TFs in the desired order
unique_elts (list[str]) – All combination strings made by _tf_combo_string

Returns

A sorted list of combination strings that have a consistent ordering

Return type

list[str]

pymodulon.imodulondb.imdb_gene_hist_df(model, k, bins=20, tol=0.001)[source]

Creates the gene histogram for an iModulon

Parameters

model (IcaData) – IcaData object
k (int or str) – iModulon name
bins (int) – Number of bins in the histogram (default = 20)
tol (float) – Distance to threshold for deciding if a bar is in the iModulon (default = .001)

Returns

gene_hist_table – A dataframe for producing the histogram that is compatible with iModulonDB

Return type

DataFrame

pymodulon.imodulondb._gene_color_dict(model)[source]

Helper function to match genes to colors based on COG. Used by imdb_gene_scatter_df.

Parameters: model (IcaData) – IcaData object
Returns: Dictionary associating gene names to colors
Return type: dict

pymodulon.imodulondb.imdb_gene_scatter_df(model, k, gene_scatter_x='start')[source]

Generates a dataframe for the gene scatter plot in iModulonDB

Parameters

model (IcaData) – IcaData object
k (int or str) – iModulon name
gene_scatter_x (str) – Determines x-axis of the scatterplot

Returns

res – A dataframe for producing the scatterplot

Return type

DataFrame

pymodulon.imodulondb.generate_n_replicates_column(model)[source]

Generates the “n_replicates” column of the sample_table for iModulonDB.

Parameters: model (IcaData) – IcaData object. Will overwrite the existing column if it exists.
Returns: None
Return type: None

pymodulon.imodulondb.imdb_activity_bar_df(model, k)[source]

Generates a dataframe for the activity bar graph of iModulon k

Parameters

model (IcaData) – IcaData object
k (int or str) – iModulon name

Returns

res – A dataframe for producing the activity bar graph for iModulonDB

Return type

DataFrame

pymodulon.imodulondb._parse_regulon_string(model, s)[source]

The Bacillus microarray dataset uses [] to create unusually complicated TF strings. This function parses those, as a helper to _get_reg_genes for imdb_regulon_venn_df.

Parameters

model (IcaData) – IcaData object
s (str) – TF string

Returns

res – Set of genes regulated by this string

Return type

set

pymodulon.imodulondb._get_reg_genes(model, tf)[source]

Finds the set of genes regulated by the boolean combination of regulators in a TF string

Parameters

model (IcaData) – IcaData object
tf (str) – string of TFs separated by +, /, and/or []

Returns

reg_genes – Set of regulated genes

Return type

set[str]

pymodulon.imodulondb.imdb_regulon_venn_df(model, k)[source]

Generates a dataframe for the regulon venn diagram of iModulon k. Returns None if there is no diagram to draw

Parameters

model (IcaData) – IcaData object
k (int or str) – iModulon name

Returns

res – A DataFrame for producing the venn diagram in iModulonDB

Return type

DataFrame

pymodulon.imodulondb.get_tfs_to_scatter(model, tf_string, tfcomplex_to_genename=None, verbose=False)[source]

Parameters

model (IcaData) – IcaData object
tf_string (str or nan) – String of TFs, or np.nan
tfcomplex_to_genename (dict, optional) – dictionary pointing complex TRN entries to matching gene names in the gene table ex: {“FlhDC”:”flhD”}
verbose (bool) – Show verbose output (default: False)

Returns

res – List of gene loci

Return type

list

pymodulon.imodulondb.imdb_regulon_scatter_df(model, k, tfcomplex_to_genename=None)[source]

Parameters

model (IcaData) – IcaData object
k (int or str) – iModulon name
tfcomplex_to_genename (dict, optional) – dictionary pointing complex TRN entries to matching gene names in the gene table ex: {“FlhDC”:”flhD”}

Returns

res – A dataframe for producing the regulon scatter plots in iModulonDB

Return type

DataFrame

pymodulon.imodulondb.tf_with_links(model, tf_str)[source]

Adds links to the regulator string

Parameters

model (IcaData) – IcaData object
tf_str (str or float) – Regulator string for a given iModulon, or np.nan

Returns

res – String with links added

Return type

str

pymodulon.imodulondb.tf_with_links_brackets(model, tf_str)[source]

Adds links to the regulator string Used with the complicated bracket system in Bacillus Microarray

Parameters

model (IcaData) – IcaData object
tf_str (str or float) – Regulator string for a given iModulon, or np.nan

Returns

res – String with links added

Return type

str

pymodulon.imodulondb.imdb_imodulon_basics_df(model, k, reg_venn, reg_scatter)[source]

Generates a dataframe for the metadata of iModulon k

Parameters

model (IcaData) – IcaData object
k (int or str) – iModulon name
reg_venn (DataFrame or None) – Output of imdb_regulon_venn_df(data, k)
reg_scatter (DataFrame or None) – Output of imdb_regulon_scatter_df(data, k)

Returns

res – A dataframe of metadata for iModulon k in iModulonDB

Return type

DataFrame

pymodulon.imodulondb.make_im_directory(model, k, path_prefix='.', gene_scatter_x='start', tfcomplex_to_genename=None)[source]

Parameters

model (IcaData) – IcaData object
k (int or str) – iModulon name
path_prefix (str, optional) – Path to the dataset folder. This function creates an ‘iModulon_files/k/’ subdirectory there to store everything. (default = “.”)
gene_scatter_x (str) – Passed to imdb_gene_scatter_df() to indicate the x axis type of that plot (default = “start”)
tfcomplex_to_genename (dict, optional) – dictionary pointing complex TRN entries to matching gene names in the gene table ex: {“FlhDC”:”flhD”}

Returns

None

Return type

None

pymodulon.imodulondb.imdb_gene_activity_bar_df(model, gene_id)[source]

Parameters

model (IcaData) – IcaData object
gene_id (str) – Locus tag of gene

Returns

res – A dataframe for the activity bar of gene in iModulonDB

Return type

DataFrame

pymodulon.imodulondb.imdb_gene_im_table_df(model, g, im_table, m_bin)[source]

Generates a dataframe for the iModulon table of gene g

Parameters

model (IcaData) – IcaData object
g (str) – Gene locus tag
im_table (DataFrame) – Pre-cleaned version of data.imodulon_table
m_bin (DataFrame) – Boolean transpose version of data.M_binarized

Returns

perGene_table – A dataframe for the iModulon table of gene g in iModulonDB

Return type

DataFrame

pymodulon.imodulondb.imdb_gene_basics_df(model, g)[source]

Parameters

model (IcaData) – IcaData object
g (str) – Gene locus

Returns

res – A dataframe for the metadata of gene g in iModulonDB

Return type

DataFrame

pymodulon.imodulondb.make_gene_directory(model, g, path_prefix='.')[source]

Generates all data for gene g, stores it in a subfolder of path_prefix

Parameters

model (IcaData) – IcaData object
g (str) – Gene locus
path_prefix (str, optional) – Path to the dataset folder. This function creates a ‘gene_page_files/k/’ subdirectory there to store everything. (default = “.”)

Returns

im_df – Table containing iModulon information for the gene

Return type

DataFrame

pymodulon.imodulondb

Module Contents

Functions

`pymodulon.imodulondb`