def plot5(sg, tids, locs, edges):
sg.plot_transcript_path('ENST04')
swan.save_fig('scratch/enst04.png')
check_subset(sg, tids, edges, locs)
node_colors_ctrl = [(0, 'gray_light_blue'), (1, 'gray_yellow'),
(2, 'light_blue'), (3, 'yellow'), (4, 'yellow'),
(5, 'orange'), (6, 'gray_orange')]
curve_ctrl = [((0, 1), None), ((1, 2), None), ((2, 3), None),
((3, 4), None), ((4, 5), None), ((0, 3), 'curved'),
((4, 6), 'curved'), ((1, 4), 'curved')]
edge_color_ctrl = [((0, 1), 'gray_green'), ((1, 2), 'gray_pink'),
((2, 3), 'green'), ((3, 4), 'pink'), ((4, 5), 'green'),
((0, 3), 'gray_green'), ((4, 6), 'gray_green'),
((1, 4), 'gray_pink')]
used_edges = [(2, 3), (3, 4), (4, 5)]
check_nodes(sg.pg.loc_df, node_colors_ctrl)
check_edges(sg.pg.edge_df, edge_color_ctrl, curve_ctrl)
return sg
def plot6(sg, tids, locs, edges):
sg.plot_graph('ENSG02', indicate_dataset='a')
swan.save_fig('scratch/ensg02_dataset')
check_subset(sg, tids, edges, locs)
edgecolor_ctrl = [(0, 'k'), (1, 'k'), (2, None), (3, 'k'), (4, 'k'),
(5, 'k'), (6, 'k')]
node_colors_ctrl = [(0, 'light_blue'), (1, 'yellow'), (2, 'light_blue'),
(3, 'yellow'), (4, 'yellow'), (5, 'orange'),
(6, 'orange')]
curve_ctrl = [((0, 1), None), ((1, 2), None), ((2, 3), None),
((3, 4), None), ((4, 5), None), ((0, 3), 'curved'),
((4, 6), 'curved'), ((1, 4), 'curved')]
edge_color_ctrl = [((0, 1), 'green'), ((1, 2), 'pink'), ((2, 3), 'green'),
((3, 4), 'pink'), ((4, 5), 'green'), ((0, 3), 'green'),
((4, 6), 'green'), ((1, 4), 'pink')]
style_ctrl = [((0, 1), 'dashed'), ((1, 2), None), ((2, 3), None),
((3, 4), 'dashed'), ((4, 5), 'dashed'), ((0, 3), 'dashed'),
((4, 6), 'dashed'), ((1, 4), 'dashed')]
check_nodes(sg.pg.loc_df, node_colors_ctrl, edgecolor_ctrl)
check_edges(sg.pg.edge_df, edge_color_ctrl, curve_ctrl, style_ctrl)
return sg
def plot4(sg, tids, locs, edges):
sg.plot_transcript_path('ENST01', indicate_novel=True)
swan.save_fig('scratch/ENST01_novel.png')
check_subset(sg, tids, edges, locs)
node_colors_ctrl = [(0, 'light_blue'), (1, 'yellow'), (2, 'yellow'),
(3, 'yellow'), (4, 'yellow'), (5, 'orange'),
(6, 'gray_orange')]
edgecolor_ctrl = [(0, None), (1, None), (2, None), (3, None), (4, None),
(5, None), (6, '#999999')]
curve_ctrl = [((0, 1), None), ((1, 2), None), ((2, 3), None),
((3, 4), None), ((4, 5), None), ((0, 3), 'curved'),
((4, 6), 'curved'), ((1, 4), 'curved')]
edge_color_ctrl = [((0, 1), 'green'), ((1, 2), 'pink'), ((2, 3), 'green'),
((3, 4), 'pink'), ((4, 5), 'green'),
((0, 3), 'gray_green'), ((4, 6), 'gray_green'),
((1, 4), 'gray_pink')]
style_ctrl = [((0, 1), None), ((1, 2), None), ((2, 3), None),
((3, 4), None), ((4, 5), None), ((0, 3), None),
((4, 6), 'dashed'), ((1, 4), 'dashed')]
used_edges = [(0, 1), (1, 2), (2, 3), (3, 4), (4, 5)]
check_nodes(sg.pg.loc_df, node_colors_ctrl, edgecolor_ctrl)
check_edges(sg.pg.edge_df, edge_color_ctrl, curve_ctrl, style_ctrl)
return sg
# returns a list of genes, transcripts, and specific edges in
# the SwanGraph with novel exon skipping events
es_genes, es_transcripts, es_edges = sg.find_es_genes()
# returns a list of genes, transcripts, and specific edges in
# the SwanGraph with novel intron retention events
ir_genes, ir_transcripts, ir_edges = sg.find_ir_genes()
### Visualization
# plot a gene summary graph
sg.plot_graph('ADRM1')
# save the currently-plotted figure with the given filename and location
swan.save_fig('figures/my_gene_summary.png')
# plot a gene summary graph with novel splice sites and
# splice junctions plotted as outlined nodes and dashed edges respectively
sg.plot_graph('ADRM1', indicate_novel=True)
# plot a gene summary graph with splice sites and splice junctions
# that are present in the indicated dataset as outlined nodes
# and dashed edges respectively
sg.plot_graph('ADRM1', indicate_dataset='HepG2_1')
# plot a gene summary graph with novel splice sites and junctions
# outlined and dashed respectively
# save the figure with the given prefix
sg.plot_graph('ADRM1', indicate_novel=True, prefix='figures/adrm1')