def __init__(self, data, gene_sets, outdir="GSEA_SingleSample", sample_norm_method='rank', min_size=15, max_size=2000, permutation_num=0, weighted_score_type=0.25, scale=True, ascending=False, processes=1, figsize=(7,6), format='pdf', graph_num=20, no_plot=False, seed=None, verbose=False): self.data=data self.gene_sets=gene_sets self.outdir=outdir self.sample_norm_method=sample_norm_method self.weighted_score_type=weighted_score_type self.scale = scale self.min_size=min_size self.max_size=max_size self.permutation_num=int(permutation_num) if int(permutation_num) > 0 else 0 self.ascending=ascending self.figsize=figsize self.format=format self.graph_num=int(graph_num) self.seed=seed self.verbose=bool(verbose) self.ranking=None self.module='ssgsea' self._processes=processes self._noplot=no_plot # init logger logfile = self.prepare_outdir() self._logger = log_init(outlog=logfile, log_level=logging.INFO if self.verbose else logging.WARNING)
def __init__(self, rnk, gene_sets, outdir='GSEA_prerank', pheno_pos='Pos', pheno_neg='Neg', min_size=15, max_size=500, permutation_num=1000, weighted_score_type=1, ascending=False, processes=1, figsize=(6.5,6), format='pdf', graph_num=20, no_plot=False, seed=None, verbose=False): self.rnk =rnk self.gene_sets=gene_sets self.outdir=outdir self.pheno_pos=pheno_pos self.pheno_neg=pheno_neg self.min_size=min_size self.max_size=max_size self.permutation_num=int(permutation_num) if int(permutation_num) > 0 else 0 self.weighted_score_type=weighted_score_type self.ascending=ascending self.figsize=figsize self.format=format self.graph_num=int(graph_num) self.seed=seed self.verbose=bool(verbose) self.ranking=None self.module='prerank' self._processes=processes self._noplot=no_plot # init logger logfile = self.prepare_outdir() self._logger = log_init(outlog=logfile, log_level=logging.INFO if self.verbose else logging.WARNING)
def __init__(self, rnk, gene_sets, outdir='GSEA_prerank', pheno_pos='Pos', pheno_neg='Neg', min_size=15, max_size=500, permutation_num=1000, weighted_score_type=1, ascending=False, processes=1, figsize=(6.5,6), format='pdf', graph_num=20, no_plot=False, seed=None, verbose=False): self.rnk =rnk self.gene_sets=gene_sets self.outdir=outdir self.pheno_pos=pheno_pos self.pheno_neg=pheno_neg self.min_size=min_size self.max_size=max_size self.permutation_num=int(permutation_num) if int(permutation_num) > 0 else 0 self.weighted_score_type=weighted_score_type self.ascending=ascending self.figsize=figsize self.format=format self.graph_num=int(graph_num) self.seed=seed self.verbose=bool(verbose) self.ranking=None self.module='prerank' self._processes=processes self._noplot=no_plot # init logger mkdirs(self.outdir) _gset =os.path.split(self.gene_sets)[-1].lower().rstrip(".gmt") outlog = os.path.join(self.outdir,"gseapy.%s.%s.log"%(self.module, _gset)) self._logger = log_init(outlog=outlog, log_level=logging.INFO if self.verbose else logging.WARNING)
def __init__(self, data, gene_sets, classes, outdir='GSEA_ouput', min_size=15, max_size=500, permutation_num=1000, weighted_score_type=1, permutation_type='gene_set', method='log2_ratio_of_classes', ascending=False, processes=1, figsize=(6.5,6), format='pdf', graph_num=20, no_plot=False, seed=None, verbose=False): self.data = data self.gene_sets=gene_sets self.classes=classes self.outdir=outdir self.permutation_type=permutation_type self.method=method self.min_size=min_size self.max_size=max_size self.permutation_num=int(permutation_num) if int(permutation_num) > 0 else 0 self.weighted_score_type=weighted_score_type self.ascending=ascending self._processes=processes self.figsize=figsize self.format=format self.graph_num=int(graph_num) self.seed=seed self.verbose=bool(verbose) self.module='gsea' self.ranking=None self._noplot=no_plot # init logger logfile = self.prepare_outdir() self._logger = log_init(outlog=logfile, log_level=logging.INFO if self.verbose else logging.WARNING)
def __init__(self, indir, outdir='GSEApy_Replot', weighted_score_type=1, min_size=3, max_size=1000, figsize=(6.5, 6), graph_num=20, format='pdf', verbose=False): self.indir = indir self.outdir = outdir self.weighted_score_type = weighted_score_type self.min_size = min_size self.max_size = max_size self.figsize = figsize self.fignum = int(graph_num) self.format = format self.verbose = bool(verbose) self.module = 'replot' self.gene_sets = None self.ascending = False # init logger mkdirs(self.outdir) outlog = os.path.join(self.outdir, "gseapy.%s.%s.log" % (self.module, "run")) self._logger = log_init( outlog=outlog, log_level=logging.INFO if self.verbose else logging.WARNING)