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| import os | ||
| from graphviz import Source | ||
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| def get_absolute_path(relative_path): | ||
| script_dir = os.path.dirname(os.path.realpath(__file__)) | ||
| return os.path.join(script_dir, relative_path) | ||
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| def generate_graph_from_file(file_path, output_file=None): | ||
| # Read the content of the file | ||
| with open(file_path, 'r') as file: | ||
| graph_data = file.read() | ||
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| # Create a Source object from the Graphviz data | ||
| graph = Source(graph_data) | ||
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| # Render the graph to a file (default format is PDF, so we explicitly specify PNG) | ||
| graph.render(filename=output_file, format='png', cleanup=True) | ||
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| def test_graph_data(): | ||
| file_path = get_absolute_path('../data/gut_microbiome') | ||
| output_file = 'out/gut_microbiome' | ||
| generate_graph_from_file(file_path=file_path, output_file=output_file) | ||
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| if __name__ == '__main__': | ||
| test_graph_data() |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,122 @@ | ||
| digraph bigraph { | ||
| // adding needed attributes here | ||
| graph [nodesep=0.06, ranksep=0.06 dpi=250 overlap=false rankdir=TB size="3,7" ratio="fill"] | ||
| node [fontsize="12pt" margin=0.05 penwidth=2 shape=circle] | ||
| "('Small<br/>Intestine',)" [label=<Small<br/>Intestine>, pos="0,0!"] | ||
| "('Small<br/>Intestine', 'Duodenum')" [label=<Duodenum>, pos="0,-1!"] | ||
| "('Small<br/>Intestine', 'Duodenum', 'nutrients')" [label=<nutrients>] | ||
| "('Small<br/>Intestine', 'Duodenum', 'mucosa')" [label=<mucosa>] | ||
| "('Small<br/>Intestine', 'Duodenum', 'mucosa', 'mucus')" [label=<mucus>] | ||
| "('Small<br/>Intestine', 'Duodenum', 'mucosa', 'mucus', 'mucin')" [label=<mucin>] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Epithelium')" [label=<Epithelium>] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Epithelium', 'Goblet<br/>cells')" [label=<Goblet<br/>cells>] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota')" [label=<Microbiota>] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli')" [label=<E.coli>] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli', 'mucinase')" [label=<mucinase>] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli', 'flagella')" [label=<flagella>] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'Bacteroidetes,<br/>Firmicutes,<br/>more')" [label=<Bacteroidetes,<br/>Firmicutes,<br/>more>] | ||
| "('Small<br/>Intestine', 'Jejunum')" [label=<Jejunum>] | ||
| "('Small<br/>Intestine', 'Ileum')" [label=<Ileum>] | ||
| node [constraint=false fontsize="12pt" penwidth=2 shape=box] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Epithelium', 'Goblet<br/>cells', 'secretion')" [label=<secretion>] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli', 'chemotaxis')" [label=<chemotaxis>] | ||
| "('Small<br/>Intestine', 'Duodenum', 'uptake')" [label=<uptake>] | ||
| "('Small<br/>Intestine', 'Duodenum', 'degradation')" [label=<degradation>] | ||
| "('Small<br/>Intestine', 'Peristalsis')" [label=<Peristalsis>] | ||
| edge [arrowhead=none penwidth=2] | ||
| edge [style=filled] | ||
| "('Small<br/>Intestine', 'Duodenum', 'mucosa', 'mucus')" -> "('Small<br/>Intestine', 'Duodenum', 'mucosa', 'mucus', 'mucin')" | ||
| edge [style=filled] | ||
| "('Small<br/>Intestine', 'Duodenum', 'mucosa')" -> "('Small<br/>Intestine', 'Duodenum', 'mucosa', 'mucus')" | ||
| edge [style=invis] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Epithelium', 'Goblet<br/>cells')" -> "('Small<br/>Intestine', 'Duodenum', 'Epithelium', 'Goblet<br/>cells', 'secretion')" | ||
| edge [style=filled] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Epithelium')" -> "('Small<br/>Intestine', 'Duodenum', 'Epithelium', 'Goblet<br/>cells')" | ||
| edge [style=filled] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli')" -> "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli', 'mucinase')" | ||
| edge [style=filled] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli')" -> "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli', 'flagella')" | ||
| edge [style=invis] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli')" -> "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli', 'chemotaxis')" | ||
| edge [style=filled] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota')" -> "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli')" | ||
| edge [style=filled] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota')" -> "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'Bacteroidetes,<br/>Firmicutes,<br/>more')" | ||
| edge [style=filled] | ||
| "('Small<br/>Intestine', 'Duodenum')" -> "('Small<br/>Intestine', 'Duodenum', 'nutrients')" | ||
| edge [style=filled] | ||
| "('Small<br/>Intestine', 'Duodenum')" -> "('Small<br/>Intestine', 'Duodenum', 'mucosa')" | ||
| edge [style=filled] | ||
| "('Small<br/>Intestine', 'Duodenum')" -> "('Small<br/>Intestine', 'Duodenum', 'Epithelium')" | ||
| edge [style=filled] | ||
| "('Small<br/>Intestine', 'Duodenum')" -> "('Small<br/>Intestine', 'Duodenum', 'Microbiota')" | ||
| edge [style=invis] | ||
| "('Small<br/>Intestine', 'Duodenum')" -> "('Small<br/>Intestine', 'Duodenum', 'uptake')" | ||
| edge [style=invis] | ||
| "('Small<br/>Intestine', 'Duodenum')" -> "('Small<br/>Intestine', 'Duodenum', 'degradation')" | ||
| edge [style=filled] | ||
| "('Small<br/>Intestine',)" -> "('Small<br/>Intestine', 'Duodenum')" | ||
| edge [style=filled] | ||
| "('Small<br/>Intestine',)" -> "('Small<br/>Intestine', 'Jejunum')" | ||
| edge [style=filled] | ||
| "('Small<br/>Intestine',)" -> "('Small<br/>Intestine', 'Ileum')" | ||
| edge [style=invis] | ||
| "('Small<br/>Intestine',)" -> "('Small<br/>Intestine', 'Peristalsis')" | ||
| edge [arrowhead=dot arrowsize=0.5 penwidth=1 style=dashed] | ||
| "('Small<br/>Intestine', 'Duodenum', 'mucosa', 'mucus', 'mucin')" [label=<mucin> fontsize="12pt" margin=0.05 penwidth=2 shape=circle] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Epithelium', 'Goblet<br/>cells')" [label=<Goblet<br/>cells> fontsize="12pt" margin=0.05 penwidth=2 shape=circle] | ||
| subgraph "('Small<br/>Intestine', 'Duodenum', 'Epithelium', 'Goblet<br/>cells', 'secretion')" { | ||
| "('Small<br/>Intestine', 'Duodenum', 'mucosa', 'mucus', 'mucin')" -> "('Small<br/>Intestine', 'Duodenum', 'Epithelium', 'Goblet<br/>cells', 'secretion')" | ||
| "('Small<br/>Intestine', 'Duodenum', 'Epithelium', 'Goblet<br/>cells')" -> "('Small<br/>Intestine', 'Duodenum', 'Epithelium', 'Goblet<br/>cells', 'secretion')" | ||
| } | ||
| "('Small<br/>Intestine', 'Duodenum', 'mucosa')" [label=<mucosa> fontsize="12pt" margin=0.05 penwidth=2 shape=circle] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli', 'flagella')" [label=<flagella> fontsize="12pt" margin=0.05 penwidth=2 shape=circle] | ||
| subgraph "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli', 'chemotaxis')" { | ||
| "('Small<br/>Intestine', 'Duodenum', 'mucosa')" -> "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli', 'chemotaxis')" | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli', 'flagella')" -> "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli', 'chemotaxis')" | ||
| } | ||
| "('Small<br/>Intestine', 'Duodenum', 'nutrients')" [label=<nutrients> fontsize="12pt" margin=0.05 penwidth=2 shape=circle] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli')" [label=<E.coli> fontsize="12pt" margin=0.05 penwidth=2 shape=circle] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Epithelium')" [label=<Epithelium> fontsize="12pt" margin=0.05 penwidth=2 shape=circle] | ||
| subgraph "('Small<br/>Intestine', 'Duodenum', 'uptake')" { | ||
| "('Small<br/>Intestine', 'Duodenum', 'nutrients')" -> "('Small<br/>Intestine', 'Duodenum', 'uptake')" | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli')" -> "('Small<br/>Intestine', 'Duodenum', 'uptake')" | ||
| "('Small<br/>Intestine', 'Duodenum', 'Epithelium')" -> "('Small<br/>Intestine', 'Duodenum', 'uptake')" | ||
| } | ||
| "('Small<br/>Intestine', 'Duodenum', 'mucosa', 'mucus', 'mucin')" [label=<mucin> fontsize="12pt" margin=0.05 penwidth=2 shape=circle] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli', 'mucinase')" [label=<mucinase> fontsize="12pt" margin=0.05 penwidth=2 shape=circle] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'Bacteroidetes,<br/>Firmicutes,<br/>more')" [label=<Bacteroidetes,<br/>Firmicutes,<br/>more> fontsize="12pt" margin=0.05 penwidth=2 shape=circle] | ||
| subgraph "('Small<br/>Intestine', 'Duodenum', 'degradation')" { | ||
| "('Small<br/>Intestine', 'Duodenum', 'mucosa', 'mucus', 'mucin')" -> "('Small<br/>Intestine', 'Duodenum', 'degradation')" | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli', 'mucinase')" -> "('Small<br/>Intestine', 'Duodenum', 'degradation')" | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'Bacteroidetes,<br/>Firmicutes,<br/>more')" -> "('Small<br/>Intestine', 'Duodenum', 'degradation')" | ||
| } | ||
| "('Small<br/>Intestine', 'Duodenum')" [label=<Duodenum> fontsize="12pt" margin=0.05 penwidth=2 shape=circle] | ||
| "('Small<br/>Intestine', 'Jejunum')" [label=<Jejunum> fontsize="12pt" margin=0.05 penwidth=2 shape=circle] | ||
| "('Small<br/>Intestine', 'Ileum')" [label=<Ileum> fontsize="12pt" margin=0.05 penwidth=2 shape=circle] | ||
| subgraph "('Small<br/>Intestine', 'Peristalsis')" { | ||
| "('Small<br/>Intestine', 'Duodenum')" -> "('Small<br/>Intestine', 'Peristalsis')" | ||
| "('Small<br/>Intestine', 'Jejunum')" -> "('Small<br/>Intestine', 'Peristalsis')" | ||
| "('Small<br/>Intestine', 'Ileum')" -> "('Small<br/>Intestine', 'Peristalsis')" | ||
| } | ||
| edge [arrowhead=dot arrowsize=0.5 penwidth=1 style=dashed] | ||
| edge [arrowhead=none arrowtail=dot dir=both penwidth=1 style=dashed] | ||
| subgraph "[('Small<br/>Intestine', 'Duodenum', 'Epithelium'), ('Small<br/>Intestine', 'Duodenum', 'Microbiota'), ('Small<br/>Intestine', 'Duodenum', 'mucosa'), ('Small<br/>Intestine', 'Duodenum', 'nutrients')]" { | ||
| rank=same | ||
| "('Small<br/>Intestine', 'Duodenum', 'Epithelium')" | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota')" | ||
| "('Small<br/>Intestine', 'Duodenum', 'Epithelium')" -> "('Small<br/>Intestine', 'Duodenum', 'Microbiota')" [ordering=out style=invis] | ||
| "('Small<br/>Intestine', 'Duodenum', 'mucosa')" | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota')" -> "('Small<br/>Intestine', 'Duodenum', 'mucosa')" [ordering=out style=invis] | ||
| "('Small<br/>Intestine', 'Duodenum', 'nutrients')" | ||
| "('Small<br/>Intestine', 'Duodenum', 'mucosa')" -> "('Small<br/>Intestine', 'Duodenum', 'nutrients')" [ordering=out style=invis] | ||
| } | ||
| subgraph "[('Small<br/>Intestine', 'Duodenum', 'Epithelium', 'Goblet<br/>cells'), ('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli'), ('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'Bacteroidetes,<br/>Firmicutes,<br/>more')]" { | ||
| rank=same | ||
| "('Small<br/>Intestine', 'Duodenum', 'Epithelium', 'Goblet<br/>cells')" | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli')" | ||
| "('Small<br/>Intestine', 'Duodenum', 'Epithelium', 'Goblet<br/>cells')" -> "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli')" [ordering=out style=invis] | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'Bacteroidetes,<br/>Firmicutes,<br/>more')" | ||
| "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'E.coli')" -> "('Small<br/>Intestine', 'Duodenum', 'Microbiota', 'Bacteroidetes,<br/>Firmicutes,<br/>more')" [ordering=out style=invis] | ||
| } | ||
| } |