sc-analyses.py File Reference

Classes
class	sc-analyses.settings
	this class reads settings of the run and keeps them in its attributes if settings file in incorrect, the init method prints error and terminates application More...

Namespaces
	sc-analyses

Functions
def	sc-analyses.read_expression (expression_file, settings, min_expression=0.1, min_cells=10, log_transform=True)
	function takes expression file and settings object and returns: More...
def	sc-analyses.run_PCA (expression_table, annotation, n_components)
	runs PCA and returns: More...
def	sc-analyses.get_isoforms_correlated_with_pc (expression_table, pc, n, filename)
	save genes correlated with a PC to file More...
def	sc-analyses.annotate_df (row, df, min_dist, ax)
	create annotation label for a point on axis if it's far enough from other points used internally by plotting functions More...
def	sc-analyses.plot_2d_pca_multiplot (transformed_expression, annotation, pca, settings)
	create plot of 6 PC combinations PC1 vs PC2, PC3 vs PC4 etc. More...
def	sc-analyses.plot_2d_pca_single_plot (transformed_expression, annotation, pca, settings)
	plot cells of defined pair of PCs arguments are: More...
def	sc-analyses.plot_3d_pca (transformed_expression, annotation, settings, height=1080, width=1600)
	create 3d PCA plot using plotly library arguments are: More...
def	sc-analyses.plot_hierarchycal_clusterings (transformed_expression, annotation, settings)
	plot hierarchycal clustering arguments are: More...
def	sc-analyses.rotate_expression (transformed_expression, x, y, angle)
	rotate transformed expression matrix by defined angle used internally in order to define pseudotime arguments are: More...
def	sc-analyses.find_pseudotime (transformed_expression, annotation, pca, settings)
	function More...
def	sc-analyses.plot_gene_with_pseudotime (exp, pseudotime, transcript_id)
	plots gene expression over pseudotime arguments are: More...
def	sc-analyses.main ()
	main function when run separately, program expects following arguments: More...

Variables
list	sc-analyses.run_modes = ["find_day_correlated_pcs", "2d-pca-multiplot", "2d-pca-single", "3d-pca", "hierarchy", "pseudotime"]
	what modes can be script run in More...
list	sc-analyses.accepted_sets_with_parameter = ["color", "outline-color", "size", "name", "shape", "superimpose", "superimpose-for-spearman"]
	sets with parameter look like: operation set_name parameter for ex. More...
list	sc-analyses.accepted_sets_without_parameter = ["remove"]
	sets without parameter look like: operation set_name for ex. More...
list	sc-analyses.accepted_parameters = ["number_of_genes"]
	parameters supposed to be set once More...