reduce_coords_df_visium_hd: Reduce resolution coordinates data.frame

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Reduce resolution coordinates data.frame

Description

This function reduces a data frame of spatial coordinates for Visium HD samples by summarizing and aggregating the data at the new barcode level.

Usage

reduce_coords_df_visium_hd(coords_df_prep, fct)

Arguments

coords_df_red

The output data.frame of the prepare_coords_df_visium_hd() function.

Details

The function aggregates the spatial coordinates based on the new barcodes created in the previous step. It calculates summary statistics for each new barcode group, including:

• x_orig, y_orig: The original x and y coordinates at the new barcode level.

• col, row: The numeric values of the column and row groups.

• square_exp: The theoretical number of original spots that could fall into the new aggregated spot.

• square_count: The actual number of non-missing spots observed.

• square_perc: The relative number of observed spots as a proportion of the theoretical number.

Value

A summarized data frame with one row per new barcode, containing aggregated spatial coordinates and counts.

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.