comparison_cor: Calculates correlation between a cell and a matrix of the...

In CSAFE-ISU/cmcR: An Implementation of the 'Congruent Matching Cells' Method

Calculates correlation between a cell and a matrix of the same dimensions extracted from the cell's associated region.

Description

Calculates correlation between a cell and a matrix of the same dimensions extracted from the cell's associated region.

Usage

comparison_cor(
  cellHeightValues,
  regionHeightValues,
  fft_ccf_df,
  use = "pairwise.complete.obs"
)

Arguments

cellHeightValues	list/tibble column of x3p objects containing a reference scan's cells (as returned by comparison_cellDivision)
regionHeightValues	list/tibble column of x3p objects containing a target scan's regions (as returned by comparison_getTargetRegions)
fft_ccf_df	data frame/tibble column containing the data frame of (x,y) and CCF values returned by comparison_fft_ccf
use	argument for stats::cor

Value

A vector of the same length as the input containing correlation values at the estimated alignment between each reference cell and its associated target region

Examples

data(fadul1.1_processed,fadul1.2_processed)

cellTibble <- fadul1.1_processed %>%
comparison_cellDivision(numCells = c(8,8)) %>%
dplyr::mutate(regionHeightValues =
             comparison_getTargetRegions(cellHeightValues = cellHeightValues,
                                         target = fadul1.2_processed)) %>%
dplyr::mutate(cellPropMissing =
           comparison_calcPropMissing(heightValues = cellHeightValues),
              regionPropMissing =
           comparison_calcPropMissing(heightValues = regionHeightValues)) %>%
dplyr::filter(cellPropMissing <= .85 & regionPropMissing <= .85) %>%
dplyr::mutate(cellHeightValues =
        comparison_standardizeHeights(heightValues = cellHeightValues),
              regionHeightValues =
        comparison_standardizeHeights(heightValues = regionHeightValues)) %>%
dplyr::mutate(cellHeightValues =
                  comparison_replaceMissing(heightValues = cellHeightValues),
              regionHeightValues =
            comparison_replaceMissing(heightValues = regionHeightValues)) %>%
dplyr::mutate(fft_ccf_df = comparison_fft_ccf(cellHeightValues,
                                              regionHeightValues)) %>%
dplyr::mutate(pairwiseCompCor = comparison_cor(cellHeightValues,
                                               regionHeightValues,
                                               fft_ccf_df))

head(cellTibble)

CSAFE-ISU/cmcR documentation built on Feb. 15, 2023, 5:10 p.m.