keggtools.render#

Render object.

Classes#

Renderer

Renderer for KEGG Pathway.

Functions#

generate_embedded_html_table(items[, border, ...])

Generate HTML table in insert into label of dot node.

Module Contents#

class keggtools.render.Renderer(kegg_pathway, gene_dict=None, cache_or_resolver=None, upper_color=(255, 0, 0), lower_color=(0, 0, 255))#

Renderer for KEGG Pathway.

Parameters:

kegg_pathway (keggtools.models.Pathway)
gene_dict (dict[str, float] | None)
cache_or_resolver (keggtools.storage.Storage | str | keggtools.resolver.Resolver | None)
upper_color (tuple[int, int, int])
lower_color (tuple[int, int, int])

property cmap_downreg: list[str]#

Generated color map as list of hexadecimal strings for downregulated genes in gene dict.

Return type:: list[str]

property cmap_upreg: list[str]#

Generated color map as list of hexadecimal strings for upregulated genes in gene dict.

Return type:: list[str]

get_gene_color(gene_id, default_color=(255, 255, 255))#

Get overlay color for given gene.

Parameters:

gene_id (str) – Identify of gene.
default_color (tuple[int, int, int]) – Default color to return if gene is not found in gene_dict. Format in RGB tuple.
default_color

Returns:

Color of gene by expression level specified in gene_dict.

Return type:

str

graph: pydot.Dot#

lower_color: tuple = (0, 0, 255)#

overlay: dict[str, float]#

pathway: keggtools.models.Pathway#

render(display_unlabeled_genes=True)#

Render KEGG pathway.

Parameters:: display_unlabeled_genes (bool) – Entries in the KGML format can have space-seperated entry names. Set this parameter to False to hide the entries.
Return type:: None

resolver: keggtools.resolver.Resolver = None#

to_binary(extension)#

Export pydot graph to binary data.

Parameters:: extension (str) – Extension of file to export. Use format string like “png”, “svg”, “pdf” or “jpeg”.
Returns:: File content are bytes object.
Return type:: bytes
Raises:: TypeError – If variable with generated dot graph is not type bytes.

to_file(filename, extension)#

Export pydot graph to file.

Parameters:

filename (str) – Filename to save file at.
extension (str) – Extension of file to export. Use format string like “png”, “svg”, “pdf” or “jpeg”.

Return type:

None

to_string()#

Pydot graph instance to dot string.

Returns:: Generated dot string of pathway.
Return type:: str

upper_color: tuple = (255, 0, 0)#

keggtools.render.generate_embedded_html_table(items, border=0, cellborder=1, truncate=None)#

Generate HTML table in insert into label of dot node.

generate_embedded_html_table({“gene1”: “#ffffff”, “gene2”: “#454545”})

Parameters:

items (dict[str, str]) – Items are dicts with have format {name: hex_color}.
border (int) – Thickness of table border. (Default: 0)
cellborder (int) – Thickness of cell border within the table. (Default: 1)
truncate (Optional[int]) – Maximal number of items in table. Set to None to disable trunaction. (Default: None)
items

Returns:

Returns html string of table.

Return type:

str