.Rhistory

source("~/Desktop/dlp_plots/script/make_cell_copynumber_tree_heatmap.R", echo=TRUE)
source("~/Desktop/dlp_plots/script/dlp_utils.R", echo=TRUE)
setwd("~/Desktop/dlp_plots")
script_dir <- './script/'
## dir to keep results of heatmap
results_dir <- './hdb_result/'
## where to keep filtered copy number state file
input_dir <- './input/'
## For meta data, heatmap plot, loading metadata file from input directory folder
grouping_file <- paste0(input_dir,'library_groupings.csv')
set.seed(1)
libs_id <- c("SC-8888") #input the analysis ticket you want to analyse
source(paste0(script_dir,'hdbscan_utils.R'))
source(paste0(script_dir,'make_cell_copynumber_tree_heatmap.R'))
set.seed(1)
libs_id <- c("SC-8888") #input the analysis ticket you want to analyse
source(paste0(script_dir,'dlp_utils.R'))
source(paste0(script_dir,'make_cell_copynumber_tree_heatmap.R'))
for(library_id in libs_id){
# For each library, generate a heatmap of tree and copy number profile
# Noted: can combine different libraries into one file first, and run this script.
hdbscran_viz(library_id, grouping_file, results_dir, input_dir)
}
setwd("~/Desktop/dlp_plots")
script_dir <- './script/'
## dir to keep results of heatmap
results_dir <- './hdb_result/'
## where to keep filtered copy number state file
input_dir <- './input/'
## For meta data, heatmap plot, loading metadata file from input directory folder
grouping_file <- paste0(input_dir,'library_groupings.csv')
set.seed(1)
libs_id <- c("SC-8888") #input the analysis ticket you want to analyse
source(paste0(script_dir,'dlp_utils.R'))
source(paste0(script_dir,'make_cell_copynumber_tree_heatmap.R'))
for(library_id in libs_id){
# For each library, generate a heatmap of tree and copy number profile
# Noted: can combine different libraries into one file first, and run this script.
hdbscran_viz(library_id, grouping_file, results_dir, input_dir)
}