View source: R/nearest_neighbor.R
NN_G | R Documentation |
For a given cell type, this function computes proportion of cells that have nearest neighbor less than r for the observed and permuted point processes.
NN_G(
mif,
mnames,
r_range = seq(0, 100, 50),
num_permutations = 50,
edge_correction = "rs",
keep_perm_dis = FALSE,
workers = 1,
overwrite = FALSE,
xloc = NULL,
yloc = NULL
)
mif |
An MIF object |
mnames |
Character vector of marker names to estimate degree of nearest neighbor distribution |
r_range |
Numeric vector of potential r values this range must include 0. |
num_permutations |
Numeric value indicating the number of permutations used. Default is 50. |
edge_correction |
Character value indicating the type of edge correction to use. Options include "rs" or "hans". |
keep_perm_dis |
Logical value determining whether or not to keep the full distribution of permuted G values |
workers |
Integer value for the number of workers to spawn |
overwrite |
Logical value determining if you want the results to replace the current output (TRUE) or be to be appended (FALSE). |
xloc |
a string corresponding to the x coordinates. If null the average of XMin and XMax will be used |
yloc |
a string corresponding to the y coordinates. If null the average of YMin and YMax will be used |
Returns a data.frame
Theoretical CSR |
Expected value assuming complete spatial randomnessn |
Permuted CSR |
Average observed G for the permuted point process |
Observed |
Observed valuefor the observed point process |
Degree of Clustering Permuted |
Degree of spatial clustering where the reference is the permuted estimate of CSR |
Degree of Clustering Theoretical |
Degree of spatial clustering where the reference is the theoretical estimate of CSR |
#Create mif object
library(dplyr)
x <- create_mif(clinical_data = example_clinical %>%
mutate(deidentified_id = as.character(deidentified_id)),
sample_data = example_summary %>%
mutate(deidentified_id = as.character(deidentified_id)),
spatial_list = example_spatial,
patient_id = "deidentified_id",
sample_id = "deidentified_sample")
# Define the set of markers to study
markers <- c("CD3..Opal.570..Positive","CD8..Opal.520..Positive",
"FOXP3..Opal.620..Positive","CD3..CD8.","CD3..FOXP3.")
# Nearest Neighbor distribution for all markers with a neighborhood size
# of 10,20,...,100 (zero must be included in the input).
x <- NN_G(mif = x, mnames = markers[1:2], num_permutations = 1,
edge_correction = 'rs', r = seq(0,100,10),
keep_perm_dis = FALSE, workers = 1)
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