Demo/Demo.md

In TrakhtenbergLab/CellTools: CellTools

Demo

Install CellTools

start_time <- Sys.time()
devtools::install_github("TrakhtenbergLab/CellTools")
end_time <- Sys.time()
end_time-start_time

[1] Time difference of 48.56251 secs

Read reference and query seurat object files into the R

reference <- readRDS(“../vignette_data/reference.rds”) 
query <- readRDS(“../vignette_data/query.rds”)

The reference and query datasets can be downloaded at https://basespace.illumina.com/s/L6R0Dqm6r7R6. The Atlas dataset, from which the reference and query datasets were generated, is also available for download at that link.

Find the optimal k-weight parameter for KNN

start_time <- Sys.time()
reference <- OptiK(reference, lab = "type", range = c(5,50), dims = 50, perc = 0.2)
end_time <- Sys.time()
end_time-start_time

[1] Time difference of 17.58038 mins

reference@misc$CellTools$opti_k

[1] 19

Denoise the Atlas Seurat Object

start_time <- Sys.time()
reference <- DeNoise(ref = reference, lab = "type", coef = 1.5)
end_time <- Sys.time()
end_time-start_time

[1] Time difference of 22.7701 secs

Map query Seurat object to reference Seurat object

start_time <- Sys.time()
result<-MapTo(reference,query,lab="type",k=19, dims=50)
end_time <- Sys.time()
end_time-start_time

[1] Time difference of 15.09316 mins

Accuracy of mapping query object to reference object

length(which(result$predicted.id == result$type))/ncol(result)

[1] 0.9833059

Optimized Tracing of Query to Reference Data

start_time <- Sys.time()
correlation<-GlobalProbe(reference,lab="type")
end_time <- Sys.time()
end_time-start_time

[1] Time difference of 1.795279 mins

TrakhtenbergLab/CellTools documentation built on Aug. 21, 2023, 2:39 p.m.