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XiaoTaoWang / NeoLoopFinder

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
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genes overlapping in visualization #59

Open ninashenker opened 8 months ago

ninashenker commented 8 months ago

Hi,

Thanks for the good work! Do you have any suggestions to how I can get the genes to not overlap with each other? Can you remove the gene schematic? I want to view 1 kb window on each side and I tried changing to the gene schematic to white but it's still hard to visualize.

clr = cooler.Cooler(mcool)
vis = Triangle(clr, assembly, n_rows=3, figsize=(7, 4.2), track_partition=[5, 0.4, 0.5], correct='weight', span=span, slopes={(0,0):1, (0,1):0.3, (1,1):1}) vis.matrix_plot(vmin=0) vis.plot_chromosome_bounds(linewidth=2) vis.plot_loops(neoloops, face_color='none', marker_size=100, cluster=False, filter_by_res=True, onlyneo=True) vis.plot_genes(release=103, fontsize=5, color='white', border_color='white', style='base') vis.plot_chromosome_bar(name_size=10, coord_size=9)

Also what is the cut-off that determines whether the gene names are displayed or not? Some of my images don't display the names at all just the schematic.

Example of image: Chordoma-0RU22033C2-Arima_25K_C2_inversion_1MB.pdf

Thanks so much! Nina

XiaoTaoWang commented 7 months ago

Hi, sorry for the delay. When you plot genes using plot_genes, you can use the parameter filter_ to determine which genes to plot within current region (all other genes not in filter_ will be excluded). You can also use the parameter label_aligns to fine tune the position of the gene names.

ninashenker commented 7 months ago

@XiaoTaoWang Thanks for your response. However, I don't want to filter any of the genes out for now. Is there a way to remove the gene schematic and just keep the gene names?