plots package#
Submodules#
plots.figure3wayInteractions module#
Created on Thu Jun 4 09:18:15 2020
@author: marcnol
- plots.figure3wayInteractions.main()#
- plots.figure3wayInteractions.parse_arguments()#
plots.figure4Mmatrix module#
Created on Fri Jun 5 17:59:34 2020
@author: marcnol
plots 4M profiles given a list of anchors.
Can work with up to two datasets
- plots.figure4Mmatrix.main()#
- plots.figure4Mmatrix.parse_arguments()#
plots.figureCompare2Matrices module#
plots.figureHiMmatrix module#
plots.figureN_HiMmatrices module#
Created on Wed Jul 8 17:01:30 2020
plots N Hi-M matrices in a subplot @author: marcnol
- plots.figureN_HiMmatrices.main()#
- plots.figureN_HiMmatrices.makesplotHiMLineProfile(matrixSegmentAnchor, unique_barcodes, segmentLabels, c_scale=0.3, c_m='RdBu', fontsize=8)#
- plots.figureN_HiMmatrices.parse_arguments()#
- plots.figureN_HiMmatrices.plotHiMLineProfile(list_data, run_parameters, data_sets)#
- plots.figureN_HiMmatrices.plotMultipleHiMmatrices(list_data, run_parameters, data_sets)#
- plots.figureN_HiMmatrices.plotTADs(list_data, run_parameters, data_sets)#
plots.figureSingleCell module#
Created on Tue Oct 13 10:41:05 2020
@author: marcnol
produces movies and structures from single cell PWD matrices
- plots.figureSingleCell.main()#
- plots.figureSingleCell.makesPlotHistograms(him_data, run_parameters, output_filename='./HiMhistograms.png', mode='KDE', kernel_width=0.25, optimize_kernel_width=False)#
- plots.figureSingleCell.parse_arguments()#
- plots.figureSingleCell.plotTrajectories(him_data, run_parameters, outputFileNameRoot, cell_id, sc_matrix, mode='matplotlib')#
- plots.figureSingleCell.plot_sc_matrix(him_data, cell_id, run_parameters, outputFileNameRoot='sc_matrix.png', ensembleMatrix=False, searchPattern='_scMatrix:')#
- plots.figureSingleCell.plotsBarcodesEfficiencies(sc_matrix, run_parameters, unique_barcodes, outputFileNameRoot='./')#
- plots.figureSingleCell.plotsBarcodesPerCell(sc_matrix, run_parameters, outputFileNameRoot='./')#
- plots.figureSingleCell.plotsRgvalues(him_data, nRows, run_parameters, output_filename='./RgValues.png', min_number_pwd=6, threshold=6, bandwidths=array([0.03162278, 0.0379269, 0.04548778, 0.05455595, 0.06543189, 0.078476, 0.0941205, 0.11288379, 0.13538762, 0.16237767, 0.1947483, 0.23357215, 0.28013568, 0.33598183, 0.40296113, 0.48329302, 0.5796394, 0.6951928, 0.83378222, 1.]))#
- plots.figureSingleCell.plotsSubplot_sc_matrices(him_data, nRows, output='subplotMatrices.png')#
- plots.figureSingleCell.returnCellsHighestNumberPWD(sorted_values, n)#
- plots.figureSingleCell.visualize2D(coordinateList, colors=[], cmap='hsv', titles=[], output='visualize2D.png')#
- plots.figureSingleCell.visualize3D(coordinates, colors=[], cmap='hsv', title=[], output='visualize3D.png')#
plots.plot_bootstrapping module#
plots.plotting_functions module#
Created on Mon Sep 4 10:34:59 2023
@author: marcnol
- plots.plotting_functions.Wilcoxon_matrix(m1, m2, uniqueBarcodes)#
- plots.plotting_functions.bootstrapping(x, N_bootstrap=9999)#
- plots.plotting_functions.bootstraps_matrix(m, N_bootstrap=9999)#
- plots.plotting_functions.gets_matrix(run_parameters, scPWDMatrix_filename='', uniqueBarcodes='')#
- plots.plotting_functions.normalize_matrix(m1, m2, mode='none')#
- plots.plotting_functions.plot_2d_matrix_simple(ifigure, matrix, unique_barcodes, yticks, xticks, cmtitle='probability', c_min=0, c_max=1, c_m='coolwarm', fontsize=12, colorbar=False, axis_ticks=False, n_cells=0, n_datasets=0, show_title=True, fig_title='')#
- plots.plotting_functions.plot_Wilcoxon_matrix(m1, m2, uniqueBarcodes, normalize=1, ratio=True, c_scale=0.6, axisLabel=True, fontsize=22, axis_ticks=False, outputFileName='', fig_title='', plottingFileExtension='.png', n_cells=0, cmap='RdBu')#
- plots.plotting_functions.plot_matrix_difference(m1, m2, uniqueBarcodes, normalize='none', ratio=True, c_scale=0.6, axisLabel=True, fontsize=22, axis_ticks=False, outputFileName='', fig_title='', plottingFileExtension='.png', n_cells=0, cmap='RdBu')#
- plots.plotting_functions.plot_mixed_matrix(m1, m2, uniqueBarcodes, normalize='none', axisLabel=False, fontsize=22, axis_ticks=False, cAxis=0.6, outputFileName='', fig_title='', plottingFileExtension='.png', n_cells=0, cmap='RdBu')#