diff --git a/README.md b/README.md
index 1f94d36..202cf1e 100644
--- a/README.md
+++ b/README.md
@@ -30,7 +30,7 @@ To install TCT as a python library:
```bash
pip install TCT
-# TCT is in development, to get the most recent update, user can install it throught the github repo
+# TCT is in development, to get the most recent update, user can install it through the github repo
```
**This the recommended approach for installation.**
@@ -90,8 +90,8 @@ API should be developed following the standard from [TRAPI](https://github.com/N
An example notebook for add a user's API can be found [here](https://github.com/NCATSTranslator/Translator_component_toolkit/blob/main/notebooks/Connecting_userAPI.ipynb).
**Note: It does not work if no user' API is established**
-### Visulize the results
-After each pipleline, it will generate a result file for visualization. A user can use **[the Visualization html](https://github.com/NCATSTranslator/Translator_component_toolkit/blob/main/notebooks/visulize_path_finder_results.html)** file to visulaize the results.
+### Visualize the results
+After each pipeline, it will generate a result file for visualization. A user can use **[the Visualization html](https://github.com/NCATSTranslator/Translator_component_toolkit/blob/main/notebooks/visulize_path_finder_results.html)** file to visulaize the results.
## Key Translator components
Connecting to key Translator components can be found [here](https://github.com/NCATSTranslator/Translator_component_toolkit/blob/main/TranslatorComponentsIntroduction.md)
diff --git a/TCT/TCT.py b/TCT/TCT.py
index d0d22ea..48434f4 100644
--- a/TCT/TCT.py
+++ b/TCT/TCT.py
@@ -3,7 +3,6 @@
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
-import ipycytoscape
import networkx as nx
import numpy as np
#import openai
@@ -1875,6 +1874,7 @@ def plot_graph_by_predicates(for_plot):
]
+ import ipycytoscape
undirected = ipycytoscape.CytoscapeWidget()
undirected.graph.add_graph_from_networkx(graph)
undirected.set_layout(title='Path', nodeSpacing=80, edgeLengthVal=50, )
@@ -1923,6 +1923,7 @@ def plot_graph_by_infores(for_plot):
]
+ import ipycytoscape
undirected = ipycytoscape.CytoscapeWidget()
undirected.graph.add_graph_from_networkx(graph)
undirected.set_layout(title='Path', nodeSpacing=80, edgeLengthVal=50, )
@@ -1971,6 +1972,7 @@ def plot_graph_by_API(for_plot):
]
+ import ipycytoscape
undirected = ipycytoscape.CytoscapeWidget()
undirected.graph.add_graph_from_networkx(graph)
undirected.set_layout(title='Path', nodeSpacing=80, edgeLengthVal=50, )
@@ -2258,6 +2260,7 @@ def visulize_path(input_node1_id, intermediate_node, input_node3_id, result, res
}},
]
+ import ipycytoscape
pathgraph = ipycytoscape.CytoscapeWidget()
pathgraph.graph.add_graph_from_networkx(graph)
pathgraph.set_layout(title='Path', nodeSpacing=80, edgeLengthVal=50, )
diff --git a/TCT/TCT_network_annotator.py b/TCT/TCT_network_annotator.py
index ce012c1..c0b1d0a 100644
--- a/TCT/TCT_network_annotator.py
+++ b/TCT/TCT_network_annotator.py
@@ -169,7 +169,7 @@ def network_annotator(gene_list,
def get_connected_graph(result_parsed, input_identifiers):
"""
- This function is used to extract the connected graph from the returned graph based on neiborhood finder from multiple inputs.
+ This function is used to extract the connected graph from the returned graph based on neighborhood finder from multiple inputs.
It will only include the input nodes and the nodes that are connected to the input nodes with degree greater than 1.
@@ -269,4 +269,4 @@ def get_connected_graph(result_parsed, input_identifiers):
if key not in selected_nodes:
del result_parsed_copy['knowledge_graph']['nodes'][key]
- return result_parsed_copy
\ No newline at end of file
+ return result_parsed_copy
diff --git a/docs/source/index.rst b/docs/source/index.rst
index fedb998..62ee746 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -22,6 +22,7 @@ Welcome to Translator Component Toolkit's documentation!
neighborhood
pathfinder
network_annotator
+ node_annotator
Indices and tables
==================
diff --git a/pyproject.toml b/pyproject.toml
index 1c31044..9365cd9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -37,7 +37,6 @@ dependencies = [
'igraph',
'pyvis',
'zstandard',
- 'copy'
]
[project.scripts]