---
title: "RLSeq Report"
subtitle: "<strong>`r object@metadata$sampleName`</strong>"
date: "`r Sys.Date()`"
output: 
  html_document:
    css: "report_style.css"
    theme: "flatly"
    toc: true
    toc_float:
      collapsed: false
      smooth_scroll: false 
    toc_depth: 2
    code_download: true
    includes:
      in_header: "header.html"
params:
  object: "placeholder"
---

<img src="https://rlbase-data.s3.amazonaws.com/misc/assets/whitebgRLSeq+Logo.png" align="right" alt="logo" width="220" style = "border: none; float: right;">

```{r setup, include=FALSE, echo=FALSE}

# Setup chunk options
knitr::opts_chunk$set(
  warning = FALSE,
  message = FALSE,
  cache = FALSE,
  echo = FALSE
)

# Libraries
library(dplyr)
library(RLSeq)

# Enable
DT::datatable(matrix(), extensions="Buttons")

# Wrangle results and trigger conditional templates
object <- params$object
rlres <- object@metadata$results
rlreslst <- lapply(slotNames(rlres), function(sn) {
  tryCatch(rlresult(object, sn), error = function(e) {NULL})
})
names(rlreslst) <- slotNames(rlres)
res_order <- c(
  "rlfsRes", "predictRes", 
  "noiseAnalysis",
  "featureEnrichment", 
  "txFeatureOverlap",
  "correlationMat", "geneAnnoRes", "rlRegionRes"
)
funcs <- c(
  "analyzeRLFS", "predictCondition", 
  "noiseAnalyze",
  "featureEnrich", 
  "txFeatureOverlap",
  "corrAnalyze", "geneAnnotation", "rlRegionTest"
)
names(res_order) <- c(
  "RLFS analysis", 
  "Sample classification",
  "Noise analysis",
  "Feature enrichment test",
  "Transcript feature overlap",
  "Correlation analysis",
  "Gene annotations",
  "RL-Regions test"
)
rlreslst <- rlreslst[res_order]
isnull <- vapply(rlreslst, is.null, FUN.VALUE = logical(1))
```

# Summary

This report was generated with **RLSeq v`r packageVersion("RLSeq")`**.

### Sample information

Sample name: <strong>`r object@metadata$sampleName`</strong>

Sample type: <strong>`r object@metadata$mode`</strong>

Label: <strong>`r object@metadata$label`</strong>

Genome: <strong>`r GenomeInfoDb::genome(object)[1]`</strong>

Time: <strong>`r date()`</strong>

### Results summary

```{r}
dplyr::tibble(
  Result = paste0("<a href=\"#", res_order,"\">", names(res_order), "</a>"),
  Available = ! isnull
) %>%
  kableExtra::kbl(escape = FALSE) %>%
  kableExtra::kable_material(c("striped", "hover")) %>%
  kableExtra::column_spec(
    column = 1,
    bold = TRUE
  ) %>%
  kableExtra::column_spec(
    column = 2,
    color = ifelse(! isnull, "black", "grey"),
    bold = ! isnull
  ) 
```

# Results

```{r childRMD, results='asis'}
rmdlst <- lapply(
    seq(res_order),
    function(i) {
        resAnchor <- res_order[i]
        func <- funcs[i]
        if (isnull[i]) {
            knitr::knit_child(
                text=c(
                    '## `r i`. `r names(resAnchor)` {#`r resAnchor`}',
                    '',
                    paste0('*Unavailable*. Run `', func,
                           '()` and then `report()` again to view this result.'),
                    '',
                    '***',
                    ''
                ),
                envir = environment(), 
                quiet = TRUE
            )
        } else {
            knitr::knit_child(
                system.file(
                    "Rmd",
                    paste0(resAnchor, ".Rmd"),
                    package = "RLSeq"
                ), 
                envir = environment(), 
                quiet = TRUE
            )
        }
    }
)
cat(unlist(rmdlst), sep = "\n")
```

# Other

> For more information about *RLSeq* please visit the package homepage [here](https://github.com/Bishop-Laboratory/RLSeq){target="_blank"}.

**Note**: if you use *RLSeq* in published research, please reference:

> Miller et al., RLSeq, (2021), GitHub repository, [Bishop-Laboratory/RLSeq](https://github.com/Bishop-Laboratory/RLSeq){target="_blank"}

## Session info

<details>

<summary>Session info</summary>

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

</details>

&nbsp;
<hr />
<p style="text-align: center;">RLSeq © `r format(Sys.Date(), "%Y")`, <a href="https://gccri.bishop-lab.uthscsa.edu/"  target="_blank">Bishop Lab</a>, UT Health San Antonio</p>
<p style="text-align: center;">RLSeq maintainer: <span style="color: #808080;"><em><a href="mailto:millerh1@uthscsa.edu">Henry Miller</a></em></span></p>

&nbsp;
