ecotyper.io¶

Readers for EcoTyper’s user-facing inputs and conversion to AnnData.

The readers reproduce how the R scripts read the same files (read.delim for bulk/Visium matrices and annotations, data.table::fread for scRNA-seq matrices), including R’s number parsers, so that a Python run starts from bit-identical values.

Functions

`annotation_from_anndata`(adata)
`from_anndata`(adata[, layer])	AnnData → genes x samples DataFrame (dense).
`read_annotation`(path)	`read.delim(annotation)`; `None` if `path` is None/"NULL"/missing.
`read_bulk_matrix`(path)	`read.delim(path); rownames(data) = data[,1]; data = data[,-1]`.
`read_fractions`(path)	CIBERSORTx fractions (`read_fractions` in lib/misc.R): columns up to (excluding) `P.value` are kept.
`read_scrna_matrix`(path)	`fread(path, data.table = F)`, then drop NA and duplicated gene names (`read_scRNA` in lib/scRNA.R).
`to_anndata`(expr[, annotation])	Genes x samples DataFrame (+ annotation with an `ID` column) → AnnData with samples/cells as `obs` and genes as `var`.

ecotyper.io.read_bulk_matrix(path)[source]¶

read.delim(path); rownames(data) = data[,1]; data = data[,-1].

Returns a genes x samples DataFrame; sample names go through make.names as in R (check.names = TRUE).

Return type:: DataFrame

ecotyper.io.read_scrna_matrix(path)[source]¶

fread(path, data.table = F), then drop NA and duplicated gene names (read_scRNA in lib/scRNA.R). Column names are kept verbatim.

Return type:: DataFrame

ecotyper.io.read_annotation(path)[source]¶

read.delim(annotation); None if path is None/”NULL”/missing.

Return type:: DataFrame | None

ecotyper.io.read_fractions(path)[source]¶

CIBERSORTx fractions (read_fractions in lib/misc.R): columns up to (excluding) P.value are kept.

Return type:: DataFrame

ecotyper.io.to_anndata(expr, annotation=None)[source]¶

Genes x samples DataFrame (+ annotation with an ID column) → AnnData with samples/cells as obs and genes as var.

Parameters:

expr (DataFrame)
annotation (DataFrame | None)

ecotyper.io.from_anndata(adata, layer=None)[source]¶

AnnData → genes x samples DataFrame (dense).

Parameters:: layer (str | None)
Return type:: DataFrame

ecotyper.io.annotation_from_anndata(adata)[source]¶

Return type:: DataFrame