adataviz.tools module

adataviz.tools.cal_stats(adata_path, obs1, modality='RNA', expression_cutoff=0, use_raw=False, normalize_per_cell=True, clip_norm_value=10, sum_only=False)

adataviz.tools.cal_tpm(adata, target_sum=1000000.0, length_fillna=1000)

adataviz.tools.composition(obs, groupby, stratify_col=None, composition_col='Region', outname=None, parent_col=None, sort_cols=None, adata=None, color_palette=None)

adataviz.tools.downsample_adata(adata_path, groupby='Group', obs_path=None, outfile='Group.downsample_1500.h5ad', downsample=1500)

adataviz.tools.export_pseudobulk_adata(adata, outdir='pseudobulk.bed', use_raw=False)

Export pseudobulk adata to bed

adataviz.tools.get_color_palette(adata, groupby='Group')

adataviz.tools.get_markers(adata_path, levels, gtf, obs=None, outdir='markers', topn=20, downsample=2000)

adataviz.tools.get_markers_worker(adata1, obs, level, df_gene, key, outdir, topn, downsample)

adataviz.tools.get_obs(adata_path, add_coord=True, usecols=None, index_name='cell', outfile=None)

adataviz.tools.load_adata(adata, backed='r')

adataviz.tools.load_color_palette(palette_path=None, adata=None, groups=[])

adataviz.tools.load_obs(obs)

adataviz.tools.merge_adata_regions(pseudobulk_adata_path, bin_size=5000, use_raw=True, res=100000, filter_chroms=True, boundary=None, exclude_chroms=['chrY', 'chrM', 'chrX'])

Aggregrate 5kb RNA or ATAC adata into 100kb (25kb, or 10kb)

Parameters:

• pseudobulk_adata_path (path)

• bin_size (int)

• use_raw

• res (int) – 100000

• filter_chroms (bool) – True

• Returns – A dataframe

• -------

adataviz.tools.normalize_adata(adata, embedding=True, outfile=None, n_top_genes=5000, n_pcs=50, batch_col=None)

adataviz.tools.prepare_color_palette(color_dict=None, outpath='palette.xlsx')

Generating a .xlsx file including all color palette.

Parameters:

colors (dict) – A dict of dict, keys are categorical terms, values are HEX color code

adataviz.tools.scrna2pseudobulk(adata_path, downsample=2000, obs_path=None, groupby='Group', use_raw=True, n_jobs=1, normalization=None, target_sum=1000000.0, gtf=None, save=None)

adataviz.tools.stat_pseudobulk(adata_path, downsample=2000, obs_path=None, groupby='Group', use_raw=False, expression_cutoff=0, modality='RNA', n_jobs=1, normalize_per_cell=True, clip_norm_value=10, save=None)

adataviz.tools.taxonomy(obs, levels=['Neighborhood', 'Class', 'Subclass', 'Group'], groupby='Region', outfile=None)

_summary_

Parameters:

obs (path or dataframe) – path to obs file (tsv, csv or h5ad) or obs dataframe with _description_