The goal of plotATLAS is to plot data from various outputs produced from the ATLAS (Analysis Tools for Low-coverage and Ancient Samples) pipleline.
You can install the development version of plotJSON from GitHub with:
# install.packages("devtools")
devtools::install_github("pandeyaparna2022/plotATLAS")Alternatively you can also use the pak package:
# install.packages("pak")
pak::pak("pandeyaparna2022/plotATLAS")Or the remotes package:
# install.packages("remotes")
remotes::install_github("pandeyaparna2022/plotATLAS", build_vignettes = TRUE)- rjson
- ggplot2
- rlang
- stringr
library(plotATLAS)
# Assign path to the input file e.g path = "path/to/folder/ATLAS_data_RGInfo.json"
path <- list_example("test.json") #here the path is the internal test data provided with the package
# define readGroups if you wish to plot only certain readGroups
readGroups <- c("ERR8666961", "ERR8684188")
# define Side 5, 3 or both. Default is both.
side = 5
# plot PMD
plot_PMD(path, side, readGroups=readGroups)
plot_PMD(path, readGroups=readGroups)
plot_PMD(path)
library(plotATLAS)
# Assign path to the input file e.g path = "path/to/folder/ATLAS_data_RGInfo.json"
path <- list_example("test.json")
# define readGroups if you wish to plot only certain readGroups
readGroups <- c("ERR8666961", "ERR8684188")
#Plot covariates
Covariates = list('quality','position','context','fragmentLength','mappingQuality','rho')
for (i in Covariates){
plot_SeqError_covariate(path,i,1);
}
### Plot BAMDiagnostic Histograms
library(plotATLAS)
# Assign path to the directory with input files e.g path = "path/to/folder/Bamdiagnostic"
path <- list_example_folder()
plot_BAMdiagnostic(path, output_directory_name = getwd())
#> [1] "The following 1 file/s are excluded because either they are empty or do not align with the required format."
#> [1] "C:\\Users\\pandapar\\AppData\\Local\\R\\win-library\\4.4\\plotATLAS\\extdata/modern_2_fragmentLengthHistogram.txt"
#> png
#> 2