itpseq.Sample

class itpseq.Sample(*, labels: dict, reference=None, dataset=None, data=None, keys=('sample',), **kwargs)

Represents a sample in a dataset, its replicates, reference, and associated metadata.

The Sample class is used to encapsulate information and behavior related to samples in a dataset. It manages details like labels, references, replicates, and metadata, and provides methods for analyzing replicates, performing differential enrichment analysis, and creating visualizations.

Attributes:
name_ref
name_vs_ref

Methods

get_counts_ratio([pos, factor, exclude_empty])

get_counts_ratio_pos([pos])

Computes a DataFrame with the enrichment ratios for each ribosome position.

hmap([r, c, pos, col, transform, cmap, ...])

Generates a heatmap of enrichment for combinations of 2 positions.

hmap_grid([pos, col, transform, cmap, vmax, ...])

Creates a grid of heatmaps for all combinations of ribosome positions passed in pos.

hmap_pos([pos, cmap, vmax, center, ax])

Generates a heatmap of enrichment ratios for amino acid positions across ribosome sites.

itp_len_plot([ax, min_codon, max_codon, ...])

Generates a line plot of inverse-toeprint (ITP) counts per length.

DE

all_logos

get_counts

infos

itoeprint

load_replicates

logo

volcano

__init__(*, labels: dict, reference=None, dataset=None, data=None, keys=('sample',), **kwargs)

Methods

DE([pos, join, quiet, filter_size, multi, ...])

__init__(*, labels[, reference, dataset, ...])

all_logos([logo_kwargs])

get_counts([pos])

get_counts_ratio([pos, factor, exclude_empty])

get_counts_ratio_pos([pos])

Computes a DataFrame with the enrichment ratios for each ribosome position.

hmap([r, c, pos, col, transform, cmap, ...])

Generates a heatmap of enrichment for combinations of 2 positions.

hmap_grid([pos, col, transform, cmap, vmax, ...])

Creates a grid of heatmaps for all combinations of ribosome positions passed in pos.

hmap_pos([pos, cmap, vmax, center, ax])

Generates a heatmap of enrichment ratios for amino acid positions across ribosome sites.

infos([html])

itoeprint([plot, norm, norm_range, ...])

itp_len_plot([ax, min_codon, max_codon, ...])

Generates a line plot of inverse-toeprint (ITP) counts per length.

load_replicates()

logo([pos, logo_kwargs, ax])

volcano([pos, query, motif, ax, x, y, ...])

Attributes

itp_len

Combines the counts of inverse-toeprints (ITPs) for each length across all replicates.

name_ref

name_vs_ref

toeprint_df