def main():
gn = Granatum()
adata = gn.ann_data_from_assay(gn.get_import("assay"))
num_cells_to_sample = gn.get_arg("num_cells_to_sample")
random_seed = gn.get_arg("random_seed")
np.random.seed(random_seed)
num_cells_before = adata.shape[0]
num_genes_before = adata.shape[1]
if num_cells_to_sample > 0 and num_cells_to_sample < 1:
num_cells_to_sample = round(num_cells_before * num_cells_to_sample)
else:
num_cells_to_sample = round(num_cells_to_sample)
if num_cells_to_sample > num_cells_before:
num_cells_to_sample = num_cells_before
if num_cells_to_sample < 1:
num_cells_to_sample = 1
sampled_cells_idxs = np.sort(np.random.choice(num_cells_before, num_cells_to_sample, replace=False))
adata = adata[sampled_cells_idxs, :]
gn.add_result(
"\n".join(
[
"The assay before down-sampling has **{}** cells and {} genes.".format(
num_cells_before, num_genes_before
),
"",
"The assay after down-sampling has **{}** cells and {} genes.".format(adata.shape[0], adata.shape[1]),
]
),
type="markdown",
)
gn.export(gn.assay_from_ann_data(adata), "Down-sampled Assay", dynamic=False)
gn.commit()
def main():
gn = Granatum()
adata = gn.ann_data_from_assay(gn.get_import("assay"))
min_cells_expressed = gn.get_arg("min_cells_expressed")
min_mean = gn.get_arg("min_mean")
max_mean = gn.get_arg("max_mean")
min_disp = gn.get_arg("min_disp")
max_disp = gn.get_arg("max_disp")
num_genes_before = adata.shape[1]
sc.pp.filter_genes(adata, min_cells=min_cells_expressed)
filter_result = sc.pp.filter_genes_dispersion(
adata.X, flavor='seurat', min_mean=math.log(min_mean), max_mean=math.log(max_mean), min_disp=min_disp, max_disp=max_disp,
)
adata = adata[:, filter_result.gene_subset]
sc.pl.filter_genes_dispersion(filter_result)
gn.add_current_figure_to_results(
"Each dot represent a gene. The gray dots are the removed genes. The x-axis is log-transformed.",
zoom=3,
dpi=50,
height=400,
)
gn.add_result(
"\n".join(
[
"Number of genes before filtering: **{}**".format(num_genes_before),
"",
"Number of genes after filtering: **{}**".format(adata.shape[1]),
]
),
type="markdown",
)
gn.export(gn.assay_from_ann_data(adata), "Filtered Assay", dynamic=False)
gn.commit()
def main():
gn = Granatum()
adata = gn.ann_data_from_assay(gn.get_import('assay'))
outliers = gn.get_arg('outliers')
num_cells_before = adata.shape[0]
kept_cell_ids = adata.obs_names.drop(outliers, errors='ignore').values
adata = adata[kept_cell_ids, :]
gn.export_statically(gn.assay_from_ann_data(adata), 'Outlier removed assay')
gn.add_result(
'You removed {} outliers from {} cells, the result assay has {} cells (and {} genes).'.format(
len(outliers), num_cells_before, adata.shape[0], adata.shape[1]
),
type='markdown'
)
gn.commit()