Chapter 11 Quality Control

library(ArchR)
library(magrittr)
library(tidyverse)
set.seed(1)

11.1 Description

Quality control/statistics plot for scATAC-seq library: TSS enrichment, nFrags, Fragment length distribution

11.2 Set env and load arrow project

## Section: set default para
##################################################
addArchRThreads(threads = 16) # setting default number of parallel threads


## Section: load object
##################################################
proj <- loadArchRProject(path = "data/ArchR/ArrowProject/Merged/")

11.3 Plots

# TSS vs nFrags
df <- getCellColData(proj, select = c("log10(nFrags)", "TSSEnrichment"))
df
## DataFrame with 3000 rows and 2 columns
##                           log10(nFrags) TSSEnrichment
##                                 <array>       <array>
## 84C#ACAGCGCGTAGAAAGG-1 4.08278537031645         8.902
## 68B#TATCTGTTCAGGATCT-1 4.60680040755567          12.5
## 84B#GTTGGGCGTACCAAGG-1 4.17052573312318         4.642
## 84B#GCAGCCAGTAGGGTTG-1 4.50843544327051         8.478
## 68B#CCTGCTAGTGATCAGG-1 3.59911856505536        18.126
## ...                                 ...           ...
## 84B#CTGAATGAGGTTACAA-1 4.52650727549542        11.936
## 84B#TCGCAGGAGCTCCGGT-1 4.16893921383598        11.844
## 68B#TGACTCCTCAAGAGAT-1 3.82711068746601         5.967
## 68A#GCCATAAGTCTGGTCG-1 3.63296316816726        18.968
## 84C#TTGCAGACATCCGTAA-1 4.25309558584903         7.259
p <- ggPoint(
  x = df[, 1],
  y = df[, 2],
  labelMeans = TRUE,
  colorDensity = TRUE,
  continuousSet = "sambaNight",
  xlabel = "Log10 Unique Fragments",
  ylabel = "TSS Enrichment",
  xlim = c(log10(500), quantile(df[, 1], probs = 0.99)),
  ylim = c(0, quantile(df[, 2], probs = 0.99))
) + geom_hline(yintercept = 4, lty = "dashed") + geom_vline(xintercept = 3, lty = "dashed")

p

## TSS enrichment scores and nFrags distribution
c("TSSEnrichment", "log10(nFrags)") %>% map(~ {
   plotGroups(
    ArchRProj = proj, 
    groupBy = "Sample", 
    colorBy = "cellColData", 
    name = .x,
    plotAs = "violin",
    alpha = 0.4,
    addBoxPlot = TRUE
  )
})
## 1 
## 1
## [[1]]

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## Fragment size distribution
plotFragmentSizes(ArchRProj = proj)
## ArchR logging to : ArchRLogs/ArchR-plotFragmentSizes-124d433d2f754-Date-2021-07-26_Time-20-56-58.log
## If there is an issue, please report to github with logFile!
## ArchR logging successful to : ArchRLogs/ArchR-plotFragmentSizes-124d433d2f754-Date-2021-07-26_Time-20-56-58.log

## TSS enrichment profile
plotTSSEnrichment(ArchRProj = proj)
## ArchR logging to : ArchRLogs/ArchR-plotTSSEnrichment-124d42daec7da-Date-2021-07-26_Time-20-57-50.log
## If there is an issue, please report to github with logFile!
## ArchR logging successful to : ArchRLogs/ArchR-plotTSSEnrichment-124d42daec7da-Date-2021-07-26_Time-20-57-50.log