Network 1

import matplotlib.pyplot as plt
import networkx as nx
import pandas as pd
import matplotlib as mpl
mpl.rcParams['pdf.fonttype']=42
mpl.rcParams['ps.fonttype']=42

plt.figure(1, figsize=(7, 6.5))

G = nx.Graph()
#G = nx.star_graph(12)
df = pd.read_table("sugar-gene.txt",header=None)
df[4] = abs(df[2])
df[5] = '-'
df[df[4] < 0.6][5] = '-.-'
df[6] = round(df[2],2)

for i,row in df.iterrows():
    G.add_edge(row[1], row[0], length=row[6], weight=7)

pos = nx.spring_layout(G, seed=63)
#nx.draw(G, pos)


elarge = [(u, v) for (u, v, d) in G.edges(data=True) if ((d["length"] >= 0.6) or (d["length"] <= -0.6))]
esmall = [(u, v) for (u, v, d) in G.edges(data=True) if ((d["length"] > -0.6) and (d["length"] < 0.6))]


node_edgecolors = ['#07CCD2' if i<0 else '#E0CCD2' for i in df[2]]
node_edgecolors.insert(0, '#C7442A')


#pos = nx.spring_layout(G, seed=12)  # positions for all nodes - seed for reproducibility
#pos = nx.spring_layout(G, seed=13)
# nodes
nx.draw_networkx_nodes(G, pos, node_size=700,
                       node_color=['#C7442A', "#A0CBE2", "#A0CBE2", "#A0CBE2", "#A0CBE2",
                                     "#A0CBE2", "#A0CBE2", "#A0CBE2",
                                     "#A0CBE2", "#A0CBE2", "#A0CBE2", "#A0CBE2", "#A0CBE2"],
                       #edgecolors=node_edgecolors
                      )

# edges
nx.draw_networkx_edges(G, pos, edgelist=elarge, width=3, edge_color='#E0CCD2')
nx.draw_networkx_edges(
    G, pos, edgelist=esmall, width=3, alpha=0.5, edge_color='#07CCD2', style="dashed"
)

# node labels
nx.draw_networkx_labels(G, pos, font_size=10, font_family="sans-serif")
# edge weight labels

edge_labels = nx.get_edge_attributes(G, "length")


#font_color = ['#07CCD2' if i<0 else '#E0CCD2' for i in df[2]]
nx.draw_networkx_edge_labels(G, pos, edge_labels, font_size=8, font_family="sans-serif")



ax = plt.gca()
ax.margins(0.15)
plt.axis("off")
plt.tight_layout()
plt.savefig("sugar-gene.pdf")

/Users/yuanzan/anaconda3/lib/python3.8/site-packages/pandas/core/computation/expressions.py:20: UserWarning: Pandas requires version '2.7.3' or newer of 'numexpr' (version '2.7.1' currently installed).
  from pandas.core.computation.check import NUMEXPR_INSTALLED
<ipython-input-2-74c007cbb4fb>:15: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  df[df[4] < 0.6][5] = '-.-'

pos

{'Suc': array([-0.00445015,  0.00211237]),
 'Solyc04g076960.4': array([-1.        ,  0.15390925]),
 'Solyc05g007190.4': array([-0.87084574, -0.34897587]),
 'Solyc06g072620.4': array([-0.69126574,  0.52293721]),
 'Solyc06g072630.4': array([ 0.36578484, -0.88810311]),
 'Solyc02g071520.3': array([-0.57781417, -0.75451513]),
 'Solyc03g005880.3': array([0.86730542, 0.34989004]),
 'Solyc03g097600.3': array([ 0.71832309, -0.55112103]),
 'Solyc03g097610.3': array([-0.12289208, -0.96105373]),
 'Solyc04g064630.3': array([ 0.99466028, -0.13976562]),
 'Solyc04g064640.4': array([0.58747402, 0.76039752]),
 'Solyc01g103940.3': array([0.12045707, 0.94882179]),
 'Solyc04g074500.3': array([-0.38673685,  0.90546632])}

df

	0	1	2	3	4	5	6
0	Solyc04g076960.4	Suc	0.788059	4.410000e-38	0.788059	-	0.79
1	Solyc05g007190.4	Suc	0.574347	1.170000e-16	0.574347	-	0.57
2	Solyc06g072620.4	Suc	-0.772010	1.100000e-35	0.772010	-	-0.77
3	Solyc06g072630.4	Suc	-0.705140	1.780000e-27	0.705140	-	-0.71
4	Solyc02g071520.3	Suc	0.580767	4.450000e-17	0.580767	-	0.58
5	Solyc03g005880.3	Suc	-0.631408	9.610000e-21	0.631408	-	-0.63
6	Solyc03g097600.3	Suc	-0.666118	1.130000e-23	0.666118	-	-0.67
7	Solyc03g097610.3	Suc	-0.674703	1.850000e-24	0.674703	-	-0.67
8	Solyc04g064630.3	Suc	0.530913	4.850000e-14	0.530913	-	0.53
9	Solyc04g064640.4	Suc	0.485328	1.140000e-11	0.485328	-	0.49
10	Solyc01g103940.3	Suc	0.718192	6.870000e-29	0.718192	-	0.72
11	Solyc04g074500.3	Suc	0.651717	2.060000e-22	0.651717	-	0.65