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global.R
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global.R
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####################################
## ShinyMultiome.UiO ##
####################################
# Authors: Ankush Sharma and Akshay Akshay
# Note: If you find this code useful and utilize any part of it,
# we kindly request that you acknowledge its usage by citing the ShinyMultiomeUiO preprint.
##load libraries
library(shiny)
library(Seurat)
library(Signac)
library(patchwork)
library(ggplot2)
library(viridis)
library(shinybusy)
library(shinyBS)
library(BSgenome.Hsapiens.UCSC.hg38)
####################################
## load seurat object ##
####################################
#path to seurat oject (rds file)
#seuratObject="PBMCShinySeuratwithcicero.RDS"
seuratObject="/Users/akshay/OneDrive - Universitaet Bern/PhD/Projetcs-extra/archR_1.0/seurat/shinyarchr/pbmc1forshiny.RDS"
#load object
pbmc=readRDS(seuratObject)
####################################
## update path for fragment files ##
####################################
#path to fragment files (fragments.tsv.gz and fragments.tsv.gz.tbi)
#fragFilePath="pbmc_granulocyte_sorted_10k_atac_fragments.tsv.gz"
fragFilePath="/Users/akshay/OneDrive - Universitaet Bern/PhD/Projetcs-extra/archR_1.0/seurat/shinyarchr/pbmc_granulocyte_sorted_10k_atac_fragments.tsv.gz"
# update fragment file path
DefaultAssay(pbmc)="peaks"
frags <- Fragments(pbmc)
frags[[1]] <- UpdatePath(frags[[1]], new.path = fragFilePath)
# assign update list of fragment objects back to the assay
Fragments(pbmc) <- NULL
Fragments(pbmc) <- frags
####################################
## End of file ##
####################################