knit_atacQC_v2.qmd

---
params:
  title: title
  id: trex_id
  genome: genome
  annot: annot
date: today


title:  "`r params$title`"
author: <a href="https://trex.biotech.cornell.edu/"> Transcriptional Regulation & Expression Facility </a>
format: 
  html:
    standalone: true
    embed-resources: true
    toc: true
    toc-location: left
    toc-title: "Summary"
    grid: 
      content-mode: full
      sidebar-width: 350px
      body-width: 1600px
---

------------------------------------------------------------------------

```{=html}
<style type="text/css">
  .quarto-title-banner {
    height: 100px; /* Adjust the height value as needed */
  }
.main-container {
  max-width: 90% !important;
  margin: auto;
}
.quarto-title-meta-contents a:hover {
  color: #c44900; 
}
.trex-logo:hover {
  transform: scale(2);
  transition: transform 0.2s ease-in-out;
  transform-origin: right center;
}





</style>
```
[![](https://raw.githubusercontent.com/bixBeta/atac/main/img/trex-mini.png){.trex-logo fig-align="right"}](https://trex.biotech.cornell.edu/)

<hr>


## Fragment Size Distributions
```{r , fig.show='hold', echo=F, results='asis'}

# Begin the tabset panel
cat('::: {.panel-tabset}\n')

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

my_elements <- c("Tab 1", "Tab 2", "Tab 3")

# Loop over the elements and create a tab for each
for (element in p1) {
  cat(paste0('## ',  gsub(pattern = ".fragSize.png", replacement = "", x = basename(element)), '\n\n'))
  
  cat(paste0("![](", element , ")", "{width=800}" ))
  # Your content for each tab goes here
  #knitr::include_graphics(p1[element])
  # For example, you can include images, text, or other R outputs
  cat('\n\n')
}

# End the tabset panel
cat(':::\n')

```


## TSSE Scores 

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

```{r echo=FALSE, warning=FALSE, out.width='60%', out.height='100%'}



suppressPackageStartupMessages(library(ggplot2))
suppressPackageStartupMessages(library(plotly))

tsseScores <- readRDS("atacQC.out/tsseScores.RDS")
tsseScores.df = as.data.frame(round(unlist(tsseScores), 2))
colnames(tsseScores.df) = "value"
tsseScores.df$Samples = rownames(tsseScores.df)

# ggplotly(ggplot(data = tsseScores.df, aes(x = labels, y = value )) + geom_bar(stat = "identity") +
#   geom_text(aes(label=value), vjust=1.6, color="white", size=3.5) + ggtitle("Transcription Start Site (TSS) Enrichment Scores") +
#   xlab("Sample") + ylab("TSS Score") + scale_y_continuous() + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1)))

m <- list(
  l = 1,
  r = 1,
  b = 50,
  t = 50,
  pad = 1
)

plot_ly(data = tsseScores.df,  x = ~  Samples, y= ~ value, type = "bar",

        colors = c('#c1b8c8'),
        text = ~ value, height = 600,
        marker = list(size = 14,
                      color = '#c1b8c8',
                      line = list(width = 1)),
        hovertemplate = paste("%{x}<br>%{text}<extra>TSSE-Score</extra>")) %>%
  layout(autosize = T, margin =m, title = "Transcription Start Site (TSS) Enrichment Scores",
         scene = list(xaxis = list(title = paste0(" %")),
                      yaxis = list(title = paste0(" %"))
         ), margin = m
  ) %>% layout(legend = list(orientation = 'v', xanchor = "left"))


```




## Peaks Annotations


```{r echo=FALSE, eval=T, out.width=1000, out.height=1000, warning=FALSE}
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",
            "#736372",
            "#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 , fig.show='hold', echo=F, results='asis'}

# Begin the tabset panel
cat('::: {.panel-tabset}\n')

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

# Loop over the elements and create a tab for each
for (element in p2) {
  cat(paste0('## ',  gsub(pattern = ".narrowPeak.Distribution.png", replacement = "", x = basename(element)), '\n\n'))
  
  cat(paste0("![](", element , ")", "{width=800}" ))
  # Your content for each tab goes here
  #knitr::include_graphics(p1[element])
  # For example, you can include images, text, or other R outputs
  cat('\n\n')
}

# End the tabset panel
cat(':::\n')

```