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)