R/sample_summary.R

In cgrlab/TypeSeqHPV: TypeSeqHPV Analysis Functions and Workflows

#' **Sample Results Summary**
#'
#' The possibly() function guards against failure for all of the figures.
#' It is better to have the report be generated and troubleshoot later why the figure was absent
#'then to have the plugin fail at these steps.

sample_summary <- function(df){

    sampleSummary = df %>%
        group_by(Project) %>%
        mutate(numSamplesTested = n()) %>%
        group_by(Project, numSamplesTested, Human_Control) %>%
        summarize(count = n()) %>%
        ungroup() %>%
        spread(Human_Control, count, fill=0) %>%
        select(Project_ID = Project, `Number Samples Tested` = numSamplesTested,
               `Number Passed` = pass, `Number Failed` = failed_to_amplify) %>%
        arrange(Project_ID) %>%
        mutate(`Perc Passed` = paste0(round(`Number Passed`/`Number Samples Tested` * 100, digits=2), "%"))  %>%
        mutate(`Perc Failed` = paste0(round(`Number Failed`/`Number Samples Tested` * 100, digits=2), "%"))

    panderOptions("table.split.table", 100)
    panderOptions("table.split.cells", 5)

    pandoc.table(as_tibble(sampleSummary), style = "multiline", justify=c("right", "left", "left", "left", "left", "left"),
                 caption = "SAMPLE Summary",
                 use.hyphening=FALSE)

}