qc.atac.Rmd

---
title: "ATAC-Seq QC"
output:
  html_document:
    toc: true
    toc_float:
      collapsed: false
      smooth_scroll: true
    number_sections: false  
df_print: kable
---

<div>
<a href="https://www.rnaseqcore.vet.cornell.edu/" target="_blank" class="trex-logo"> <img src="/home/fa286/trex-extended-logo.png"
style=
"position:absolute;
top:0px;
right:0;
padding:20px;
height:140px;
text-align:justify;
display:block;
width:32%;
height:auto;
margin:0 auto 20px !important;"> </a>
</div>




<br><br><br><br><br>

***

## Fragment Size Distributions
```{r out.width=c('50%', '50%'), fig.show='hold', echo=F}

p1 <- list.files("./atacQC.out/", pattern = "fragSize.png$", full.names = T)

knitr::include_graphics(p1)

```


## TSSE Scores 

[Encode Guidelines](https://www.encodeproject.org/atac-seq/#standards)

![](atacQC.out/TSSE_scores.png){width=1000px}



```{r out.width=c('50%', '50%'), fig.show='hold', echo=F , eval=F}

p3 <- list.files("./atacQC.out/", pattern = "narrowPeak.Annotated.png$", full.names = T)

knitr::include_graphics(p3)

```


## Peak Annotations

```{r echo=FALSE, eval=T, out.width=1000, out.height=1000}
logs = list.files(path = "./atacQC.out/", pattern = "__percent__annot__log.txt$", full.names = T)

logs.list = list()
for (i in 1:length(logs)) {
  logs.list[[i]] <- read.table(logs[i], header = T, sep = "\t", row.names = 1)
  names(logs.list)[[i]] <-  gsub(pattern = "_peaks.narrowPeak__percent__annot__log.txt",
                                 replacement = "", basename(logs[[i]]))
}


logs.df <- do.call("rbind", logs.list)

suppressPackageStartupMessages(library(tidyr))
logs.df$tmp = rownames(logs.df)
logs.df = separate(logs.df, col = tmp, into = "sampleID", sep = "\\.", extra = "drop")

colors<-  c("#EF8A62",
            "#1f78b4",
            "#1b9e77",
            "khaki4",
            "#E9A3C9",
            "#A1D76A",
            "#FFFF33",
            "grey",
            "#b3e2cd",
            "#67A9CF",
            "peachpuff2",
            "red",
            "magenta3",
            "blue",
            "yellow"
)

suppressPackageStartupMessages(library(dplyr))
suppressPackageStartupMessages(library(plotly))
logs.df$Frequency = round(logs.df$Frequency, 1)
  m <- list(
      l = 50,
      r = 50,
      b = 100,
      pad = 20
    )
logs.df %>% plot_ly(x = ~Frequency, y = ~sampleID, type = 'bar', orientation = "h",
        name = ~Feature, color = ~Feature, colors =rev(colors) ) %>%
  layout(yaxis = list(title = 'Percentage(%)'), barmode = 'stack',
         legend = list(orientation = 'h', xanchor = "center",
                       x = 0.5, y = -0.1), margin = m)




```


## Read Count Frequencies

```{r out.width=c('50%', '50%'), fig.show='hold', echo=F}

p2 <- list.files("./atacQC.out/", pattern = "peaks.narrowPeak.Distribution.png$", full.names = T)

knitr::include_graphics(p2)

```