In Bishop-Laboratory/RLSeq: RLSeq: An analysis package for R-loop mapping data

# 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 vr packageVersion("RLSeq").

Sample information

Sample name: r object@metadata$sampleName

Sample type: r object@metadata$mode

Label: r object@metadata$label

Genome: r GenomeInfoDb::genome(object)[1]

Time: r date()

Results summary

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

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")