---
output: 
    html_document:
        theme: spacelab
        toc: true
        toc_float: true
        df_print: kable
        code_folding: show
    pdf_document:
        toc: true
    BiocStyle::html_document:
        toc: true
    BiocStyle::pdf_document:
        toc: true
always_allow_html: yes
editor_options: 
    chunk_output_type: console
title: "`r sampleId`"
date: "`r Sys.Date()`"
author: "`r paste0('alevinQC (v', utils::packageVersion('alevinQC'), ')')`"
---

<style>
   tbody tr:nth-child(odd){
    background-color: #D6E0F5;
  }
</style>

```{r prep, include = FALSE}
knitr::opts_chunk$set(echo = showCode, warning = FALSE, message = FALSE)
knitr::opts_knit$set(progress = FALSE, verbose = FALSE)
```

```{r setup-alevin, echo = showCode && (quantMethod == "alevin"), eval = (quantMethod == "alevin")}
## Read input files
if (!quiet) message("Reading Alevin output files...")
alevin <- readAlevinQC(baseDir = baseDir, customCBList = customCBList)
firstSelColName <- "inFirstWhiteList"
```

```{r setup-alevinfry, echo = showCode && (quantMethod == "alevin-fry"), eval = (quantMethod == "alevin-fry")}
## Read input files
if (!quiet) message("Reading Alevin-fry output files...")
alevin <- readAlevinFryQC(mapDir = mapDir, permitDir = permitDir,
                          quantDir = quantDir)
firstSelColName <- "inPermitList"
```

# Version info for `r quantMethod` run

```{r, warning = FALSE}
suppressWarnings({
    knitr::kable(
        alevin$versionTable
    )
})
```

# Summary tables

## Full set of cell barcodes

```{r, warning = FALSE}
if (!quiet) message("Generating summary tables...")
suppressWarnings({
    knitr::kable(
        alevin$summaryTables$fullDataset
    )
})
```

```{r initial-whitelist-title, echo = FALSE, results = "asis", eval = ("initialWhitelist" %in% names(alevin$summaryTables))}
cat("## Initial whitelist")
```

```{r, warning = FALSE, echo = showCode && ("initialWhitelist" %in% names(alevin$summaryTables)), eval = ("initialWhitelist" %in% names(alevin$summaryTables))}
suppressWarnings({
    knitr::kable(
        alevin$summaryTables$initialWhitelist
    )
})
```

```{r final-whitelist-title, echo = FALSE, results = "asis", eval = ("finalWhitelist" %in% names(alevin$summaryTables))}
cat("## Final whitelist")
```

```{r, warning = FALSE, echo = showCode && ("finalWhitelist" %in% names(alevin$summaryTables)), eval = ("finalWhitelist" %in% names(alevin$summaryTables))}
suppressWarnings({
    knitr::kable(
        alevin$summaryTables$finalWhitelist
    )
})
```

```{r permitlist-title, echo = FALSE, results = "asis", eval = ("permitlist" %in% names(alevin$summaryTables))}
cat("## Permitlist")
```

```{r, warning = FALSE, echo = showCode && ("permitlist" %in% names(alevin$summaryTables)), eval = ("permitlist" %in% names(alevin$summaryTables))}
suppressWarnings({
    knitr::kable(
        alevin$summaryTables$permitlist
    )
})
```

```{r custom-cb-tables-title, echo = FALSE, results = 'asis', eval = (length(customCBList) > 0)}
cat("## Custom cell barcode set(s)")
```

```{r custom-cb-tables, echo = showCode && (length(customCBList) > 0), results = "asis", eval = (length(customCBList) > 0)}
for (cbl in names(customCBList)) {
    cat(paste0("### ", cbl))
    suppressWarnings({
        print(knitr::kable(
            alevin$summaryTables[[paste0("customCB__", cbl)]]
        ))
    })
    cat("\n")
}
```

# Knee plot

```{r, results="asis", echo=FALSE, eval=(quantMethod == "alevin")}
cat(paste0("The knee plot displays the number of times each cell barcode ", 
           "is observed, indecreasing order. By finding a 'knee' in this ", 
           "plot, Alevin determines a threshold (indicated in the plot) that ", 
           "defines an initial 'whitelist' - a set of cell barcodes that ", 
           "likely represent non-empty droplets - and distinguishes them from ", 
           "the background. The initial whitelisting is only performed if no ", 
           "external whitelist is provided when running alevin. In the ", 
           "figure below, red indicates cell barcodes in the initial ", 
           "whitelist, black indicates all other cell barcodes."))
```

```{r, results="asis", echo=FALSE, eval=(quantMethod == "alevin-fry")}
cat(paste0("The knee plot displays the number of times each cell barcode ", 
           "is observed, indecreasing order. By finding a 'knee' in this ", 
           "plot, alevin-fry determines a threshold (indicated in the plot) ", 
           "that defines a 'permitlist' - a set of cell barcodes that ", 
           "likely represent non-empty droplets - and distinguishes them from ", 
           "the background. In the figure below, red indicates cell barcodes ", 
           "in the permitlist, black indicates all other cell barcodes."))
```


```{r}
if (!quiet) message("Generating knee plot...")
plotAlevinKneeRaw(alevin$cbTable, firstSelColName = firstSelColName)
```

# Cell barcode error correction and merging with initial whitelist

```{r, results="asis", echo=FALSE, eval=(quantMethod == "alevin")}
cat(paste0("Once the initial set of whitelisted cell barcodes is defined, ", 
           "Alevin goes through the remaining cell barcodes. If a cell ", 
           "barcode is similar enough to a whitelisted cell barcode, it will ", 
           "be corrected and the reads will be added to those of the ", 
           "whitelisted one. The figure below shows the original frequency ", 
           "of the whitelisted barcodes vs the frequency after this ", 
           "correction. The reads corresponding to cell barcodes that can ", 
           "not be corrected to a whitelisted barcode are discarded."))
```

```{r, results="asis", echo=FALSE, eval=(quantMethod == "alevin-fry")}
cat(paste0("Once the initial permitlist of cell barcodes is defined, ", 
           "alevin-fry goes through the remaining cell barcodes. If a cell ", 
           "barcode is similar enough to cell barcode in the permitlist, it ", 
           "will be corrected and the reads will be added to those of the ", 
           "one in the permitlist. The figure below shows the original frequency ", 
           "of the barcodes in the permitlist vs the frequency after this ", 
           "correction. The reads corresponding to cell barcodes that can ", 
           "not be corrected to a barcode in the permitlist are discarded."))
```


```{r, echo = showCode && (quantMethod == "alevin"), eval = (quantMethod == "alevin")}
if (!quiet) message("Generating barcode collapsing plot...")
plotAlevinBarcodeCollapse(alevin$cbTable, firstSelColName = firstSelColName,
                          countCol = "collapsedFreq")
```

```{r, echo = showCode && (quantMethod == "alevin-fry"), eval = (quantMethod == "alevin-fry")}
if (!quiet) message("Generating barcode collapsing plot...")
plotAlevinBarcodeCollapse(alevin$cbTable, firstSelColName = firstSelColName,
                          countCol = "nbrMappedUMI")
```

# Quantification

```{r, results="asis", echo=FALSE, eval=(quantMethod == "alevin")}
cat(paste0("After cell barcode collapsing, Alevin estimates the UMI count ", 
           "for each cell and gene. Following quantification, an additional ", 
           "cell barcode whitelisting is performed with the aim of ", 
           "extracting good quality cells, using not only the barcode ", 
           "frequency but also other features such as the fraction of mapped ", 
           "reads, the duplication rate and the average gene count. The ", 
           "plots below show the association between the cell barcode ", 
           "frequency (the number of observed reads corresponding to a ", 
           "cell barcode), the total UMI count and the number of detected ", 
           "genes. The cell barcodes are colored by whether or not they ", 
           "are included in the final whitelist."))
```

```{r, results="asis", echo=FALSE, eval=(quantMethod == "alevin-fry")}
cat(paste0("After cell barcode collapsing, alevin-fry estimates the UMI count ",
           "for each cell and gene. The plots below show the association ", 
           "between the cell barcode frequency (the number of observed ", 
           "reads corresponding to a cell barcode), the total UMI count and ", 
           "the number of detected genes. "))
```

These figures can give an indication of whether the sequenced reads actually
align to genes, as well as the duplication rate and the degree of saturation.
For many droplet data sets, the association between the barcode frequency and
the total UMI count is rougly linear, while the association of any of these with
the number of detected genes often deviates from linearity, if a small subset of
the genes are assigned a large fraction of the UMI counts.

```{r fig.width = 10, fig.height = 4, eval = (quantMethod == "alevin"), echo = showCode && (quantMethod == "alevin")}
if (!quiet) message("Generating quantification summary plot...")
plotAlevinQuant(alevin$cbTable, colName = "inFinalWhiteList",
                cbName = "final whitelist",
                firstSelColName = firstSelColName)
```

```{r fig.width = 10, fig.height = 4, eval = (quantMethod == "alevin-fry"), echo = showCode && (quantMethod == "alevin-fry")}
if (!quiet) message("Generating quantification summary plot...")
plotAlevinQuant(alevin$cbTable, colName = "inPermitList",
                cbName = "permitlist",
                firstSelColName = firstSelColName)
```

```{r custom-cb-plots-title, echo = FALSE, results = 'asis', eval = (length(customCBList) > 0)}
cat("## Custom cell barcode set(s)")
```

```{r custom-cb-plots, echo = showCode && (length(customCBList) > 0), eval = (length(customCBList) > 0), fig.width = 10, fig.height = 4}
for (cbl in names(customCBList)) {
    print(plotAlevinQuant(alevin$cbTable, colName = paste0("customCB__", cbl),
                          cbName = cbl), firstSelColName = firstSelColName)
}
```

# Knee plot, number of detected genes

Similarly to the knee plot that was used to select the initial set of cell 
barcodes, the plot below shows the number of detected genes for each cell
barcode included in the 
`r ifelse(quantMethod == "alevin", "initial whitelist", "permitlist")`, 
in decreasing order.

```{r}
if (!quiet) message("Generating knee plot for nbr genes...")
plotAlevinKneeNbrGenes(alevin$cbTable, firstSelColName = firstSelColName)
```

# Selected summary distributions

The histograms below show the distributions of the deduplication rates 
(number of deduplicated UMI counts/number of mapped reads) and the 
mapping rates, across the cells retained in the 
`r ifelse(quantMethod == "alevin", "initial whitelist", "permitlist")`.

```{r, fig.width = 10, fig.height = 4, echo = showCode && (quantMethod == "alevin"), eval = (quantMethod == "alevin")}
if (!quiet) message("Generating summary distribution plots...")
cowplot::plot_grid(
    plotAlevinHistogram(alevin$cbTable, plotVar = "dedupRate",
                        axisLabel = "Deduplication rate",
                        colName = "inFinalWhiteList",
                        cbName = "final whitelist",
                        firstSelColName = firstSelColName),
    plotAlevinHistogram(alevin$cbTable, plotVar = "mappingRate",
                        axisLabel = "Mapping rate",
                        colName = "inFinalWhiteList",
                        cbName = "final whitelist",
                        firstSelColName = firstSelColName),
    nrow = 1
)
```

```{r, fig.width = 10, fig.height = 4, echo = showCode && (quantMethod == "alevin-fry"), eval = (quantMethod == "alevin-fry")}
if (!quiet) message("Generating summary distribution plots...")
cowplot::plot_grid(
    plotAlevinHistogram(alevin$cbTable, plotVar = "dedupRate",
                        axisLabel = "Deduplication rate",
                        colName = firstSelColName,
                        cbName = "permitlist",
                        firstSelColName = firstSelColName),
    plotAlevinHistogram(alevin$cbTable, plotVar = "mappingRate",
                        axisLabel = "Mapping rate",
                        colName = firstSelColName,
                        cbName = "permitlist",
                        firstSelColName = firstSelColName),
    nrow = 1
)
```

```{r custom-cb-hists-title, echo = FALSE, results = 'asis', eval = (length(customCBList) > 0)}
cat("## Custom cell barcode set(s)")
```

```{r custom-cb-hists, echo = showCode && (length(customCBList) > 0), eval = (length(customCBList) > 0), fig.width = 10, fig.height = 4}
for (cbl in names(customCBList)) {
    print(cowplot::plot_grid(
        plotAlevinHistogram(alevin$cbTable, plotVar = "dedupRate",
                            axisLabel = "Deduplication rate",
                            colName = paste0("customCB__", cbl),
                            cbName = cbl,
                            firstSelColName = firstSelColName),
        plotAlevinHistogram(alevin$cbTable, plotVar = "mappingRate",
                            axisLabel = "Mapping rate",
                            colName = paste0("customCB__", cbl),
                            cbName = cbl,
                            firstSelColName = firstSelColName),
        nrow = 1
    ))
}
```


# Session info

```{r}
sessionInfo()
```

