added one new edge case to plottedgraph and associated test to test_p…

…lotting

swan_vis/plottedgraph.py

@@ -71,8 +71,16 @@ def init_plot_settings(self, sg,
 		else:
 			self.graph_type = 'summary'
 
+
+		# if we have new datasets
+		if len(list(set(old_dataset_cols)-set(self.dataset_cols))) != 0:
+			self.new_gene(sg)
+			if not self.browser:
+				self.calc_node_edge_styles()
+				self.get_ordered_edges()
+
 		# plotting the same transcript
-		if old_tid == self.tid and self.tid != None:
+		elif old_tid == self.tid and self.tid != None:
 			if not browser: 
 				if old_indicate_dataset != self.indicate_dataset \
 				or old_indicate_novel != self.indicate_novel:

swan_vis/swangraph.py

@@ -1044,6 +1044,8 @@ def find_ir_genes(self):
 							if len(temp_df.index) > 0:
 								ir_genes.append(gid)
 
+		print('Found {} novel ir events from {} genes.'.format(len(ir_genes), 
+			len(list(set(ir_genes)))))
 		ir_genes = list(set(ir_genes))
 		return ir_genes
 
@@ -1100,6 +1102,8 @@ def find_es_genes(self):
 							if len(temp_df.index) > 0:
 								es_genes.append(gid)
 
+		print('Found {} novel es events from {} genes.'.format(len(es_genes),
+			len(list(set(es_genes)))))
 		es_genes = list(set(es_genes))
 		return es_genes
 
@@ -1560,8 +1564,7 @@ def gen_report(self,
 			t_df = reset_dupe_index(t_df, 'tid')
 			t_df['significant'] = False
 			t_df = t_df.merge(de_df[['tid', 'qval']], how='left', on='tid')
-			t_df['significant'] = False
-			t_df['significant'] = t_df.loc[t_df.qval <= q]
+			t_df['significant'] = t_df.qval <= q
 			t_df = set_dupe_index(t_df, 'tid')
 
 		# if user doesn't care about datasets, just show all transcripts

testing/test_plotting.py

@@ -36,6 +36,27 @@ def test_plotting(self):
 		gene1_edge_df['edge_id'] = gene1_edge_df.apply(lambda x: 
 			(x.v1, x.v2), axis=1)
 
+		sg.loc_df = gene1_loc_df
+		sg.edge_df = gene1_edge_df
+		sg.t_df = gene1_t_df
+
+		sg.loc_df = create_dupe_index(sg.loc_df, 'vertex_id')
+		sg.loc_df = set_dupe_index(sg.loc_df, 'vertex_id')
+		sg.edge_df = create_dupe_index(sg.edge_df, 'edge_id')
+		sg.edge_df = set_dupe_index(sg.edge_df, 'edge_id')
+		sg.t_df = create_dupe_index(sg.t_df, 'tid')
+		sg.t_df = set_dupe_index(sg.t_df, 'tid')
+		sg.get_loc_types()
+
+		# testing
+		gene1_tids = gene1_t_df.tid.tolist()
+		gene1_locs = gene1_loc_df.vertex_id.tolist()
+		gene1_edges = gene1_edge_df.edge_id.tolist()
+
+		# 0th plot - gene summary graph of ENSG01
+		sg.datasets = ['annotation', 'a']
+		sg = plot0(sg, gene1_tids, gene1_locs, gene1_edges)
+
 		gene2_loc_df = pd.DataFrame({'chrom': [4, 4, 4, 4, 4, 4, 4],
 			'coord': [35, 30, 25, 20, 15, 10, 5],
 			'strand': ['-', '-', '-', '-', '-', '-', '-'],
@@ -76,13 +97,14 @@ def test_plotting(self):
 		sg.get_loc_types()
 
 		# testing
-		gene1_tids = gene1_t_df.tid.tolist()
-		gene1_locs = gene1_loc_df.vertex_id.tolist()
-		gene1_edges = gene1_edge_df.edge_id.tolist()
 		gene2_tids = gene2_t_df.tid.tolist()
 		gene2_locs = gene2_loc_df.vertex_id.tolist()
 		gene2_edges = gene2_edge_df.edge_id.tolist()
 
+		# remake the same plot and force it to update
+		sg.datasets = ['annotation', 'a', 'b']
+		sg = plot0_5(sg, gene2_tids, gene1_locs, gene1_edges)
+
 		# first plot - gene summary graph of ENSG01
 		sg = plot1(sg, gene1_tids, gene1_locs, gene1_edges)
 
@@ -116,6 +138,51 @@ def test_plotting(self):
 
 		# add a new dataset to the graph and plot a transcript from a different gene
 
+def plot0(sg, tids, locs, edges):
+	sg.plot_graph('ENSG01')
+	check_subset(sg, tids, edges, locs)
+	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')]
+	check_nodes(sg.pg.loc_df, node_colors_ctrl)
+	check_edges(sg.pg.edge_df, edge_color_ctrl, curve_ctrl)
+	return sg
+
+def plot0_5(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 plot1(sg, tids, locs, edges):
 	sg.plot_graph('ENSG01')
 	check_subset(sg, tids, edges, locs)