R/plate_summary.R

In NCI-CGR/TypeSeq2: TypeSeq2 HPV Analysis Functions and Workflows

#' plate_summary
#'

plate_summary <- function(samples_only_for_report, is_clinical=F,for_batch=F, output_prefix=NULL){

    require(pander)

    vv <- ifelse(! for_batch, "Assay_Batch_Code", "Project") %>% rlang::sym()

    # if samples_only_for_report is empty
    # Error: Evaluation error: object 'total_reads' not found.
    t4=data.frame()
    if(nrow(samples_only_for_report)==0){
        

    }else{
        t4 <- samples_only_for_report %>% 
            group_by(!!vv, Assay_Plate_Code) %>% 
            summarise( 
                hpv_pos_perc = fmt_perc(sum(Num_Types_Pos >0, na.rm=T) / n(), digits=1 ),
                plate_total_reads = scales::comma(sum(total_reads, na.rm = TRUE)),
                number_of_samples = n(), 
                num_samples_failed = sum(overall_qc == "fail", na.rm=T)
            ) %>% 
            dplyr::select(!!vv, 
                `Assay Plate Code` = Assay_Plate_Code,
                `HPV % Positive` = hpv_pos_perc,
                `total reads` = plate_total_reads,
                `# samples total` = number_of_samples,
                `# samples failed` = num_samples_failed,
            ) %>% when(
                    is_clinical ~  select(., -`HPV % Positive`),
                    ~ .
                )
    }

    t4 %>% pandoc.table(style = "multiline", caption = "Assay Plate Performance", split.cells = 12)

    if(!is.null(output_prefix)){
        write_csv(t4, sprintf("%s.Table4.csv", output_prefix))
    }
    
    return(t4)
}