MAFDash
In MAFDash: Create an HTML Dashboard to Visualize Data from MAF File

library(MAFDash)

maf_file <- params$maffile
title_text <- params$titletext

all_plot_opts <- params$plot_list
if (is.null(all_plot_opts)) {
  all_plot_opts = list("summary_plot"=TRUE,
                       "burden"=TRUE,
                       "oncoplot"=TRUE,
                       "cooccurence"=TRUE,
                       # "other"="custom_image.pdf",
                       "heatmap"=TRUE
                       )
}

template_dir <- getwd()
options(knitr.duplicate.label = "allow")

maf <- NULL

maf_data <- maf_file
clinical_data <- NULL

if (!is.null(maf_file)) {
  if (class(maf_file)=="MAF") {
    maf_data <- rbind(maf_file@data, maf_file@maf.silent)
    clinical_data <- maf_file@clinical.data
  }
  maf <- maftools::read.maf(maf_data, clinicalData = clinical_data,verbose = FALSE)
}

summary_table_text=NULL
if (!is.null(maf)) {
  summ_template_name=file.path(template_dir, "summary_table.Rmd")
  summary_table_text <- knitr::knit_expand(summ_template_name)
}

r paste(knitr::knit(text = paste(summary_table_text, collapse = '\n')))

Row {.tabset .tabset-fade data-height=800}

``` {r make-plot-tabs }

all_plot_opts = list("summary_plot"=TRUE,

# "burden"=TRUE,

# "oncoplot"=TRUE,

# "cooccurence"=TRUE,

# "heatmap"=TRUE,

"other"="~/Documents/my_tools/MAFdash/Rpackage/testing/custom_image.pdf"

)

out <- lapply(names(all_plot_opts), function(plotname) { plot_input <- all_plot_opts[[plotname]] if (is.logical(plot_input) && plot_input) { template_name=file.path(template_dir, paste0(plotname, ".Rmd")) if (file.exists(template_name)) { return_text <- knitr::knit_expand(template_name) } } else { tab_text <- paste0("\n### ", plotname) rchunk_text <- c("{r, out.width='100%', out.height='95%' }","") plot_text <- "print('Image not found')" if (is.character(plot_input) && file.exists(plot_input)) { plot_text <- paste0("knitr::include_graphics(all_plot_opts[['",plotname,"']])") } else if (class(plot_input)[1] %in% c("gg","Heatmap")) { plot_text <- paste0("print(all_plot_opts[['",plotname,"']])") } else if (class(plot_input)[1] %in% c("plotly")) { plot_text <- paste0("all_plot_opts[['",plotname,"']]") } return_text <- paste(tab_text, rchunk_text[1], plot_text, rchunk_text[2], sep="\n",collapse="\n") } return(return_text)

})

`r paste(knitr::knit(text = paste(out, collapse = '\n')))`

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

```r
var_table_text=NULL
if (!is.null(maf)) {
  vartbl_template_name=file.path(template_dir, "variant_table.Rmd")
  var_table_text <- knitr::knit_expand(vartbl_template_name)
}