R/expressionTCGA.R

In RTCGA: The Cancer Genome Atlas Data Integration

## RTCGA package for R
#' @title Gather Expressions for TCGA Datasets
#'
#' @description Function gathers expressions over multiple TCGA datasets and extracts expressions for desired genes.
#' See \link[RTCGA.rnaseq]{rnaseq}, \link[RTCGA.mRNA]{mRNA}, \link[RTCGA.RPPA]{RPPA}, \link[RTCGA.miRNASeq]{miRNASeq}, \link[RTCGA.methylation]{methylation}.
#'  
#' @param ... A data.frame or data.frames from TCGA study containing expressions informations. 
#' 
#' @param extract.names Logical, whether to extract names of passed data.frames in \code{...}.
#' 
#' @param extract.cols A character specifing the names of columns to be extracted with \code{bcr_patient_barcode}. 
#' If \code{NULL} (by default) all columns are returned.
#' 
#' @note Input data.frames should contain column \code{bcr_patient_barcode} if \code{extract.cols} is specified. 
#' 
#' @section Issues:
#' 
#' If you have any problems, issues or think that something is missing or is not
#' clear please post an issue on 
#' \href{https://github.com/RTCGA/RTCGA/issues}{https://github.com/RTCGA/RTCGA/issues}.
#' 
#' @author 
#' Marcin Kosinski, \email{m.p.kosinski@@gmail.com}
#' 
#' @seealso 
#' 
#' \pkg{RTCGA} website \href{http://rtcga.github.io/RTCGA/Visualizations.html}{http://rtcga.github.io/RTCGA/Visualizations.html}.
#' 
#' @examples 
#' 
#' ## for all examples
#' library(dplyr)
#' library(tidyr)
#' library(ggplot2) 
#' 
#' ## RNASeq expressions
#' library(RTCGA.rnaseq)
#' expressionsTCGA(BRCA.rnaseq, OV.rnaseq, HNSC.rnaseq,
#'                extract.cols = "VENTX|27287") %>%
#'   rename(cohort = dataset,
#'          VENTX = `VENTX|27287`) %>%  
#'  filter(substr(bcr_patient_barcode, 14, 15) == "01") %>% #cancer samples
#'   ggplot(aes(y = log1p(VENTX),
#'              x = reorder(cohort, log1p(VENTX), median),
#'              fill = cohort)) + 
#'   geom_boxplot() +
#'   theme_RTCGA() +
#'   scale_fill_brewer(palette = "Dark2")
#'   
#' ## mRNA expressions  
#' library(tidyr)
#' library(RTCGA.mRNA)
#' expressionsTCGA(BRCA.mRNA, COAD.mRNA, LUSC.mRNA, UCEC.mRNA,
#'                extract.cols = c("ARHGAP24", "TRAV20")) %>%
#'   rename(cohort = dataset) %>%
#'   select(-bcr_patient_barcode) %>%
#'   gather(key = "mRNA", value = "value", -cohort)  %>%
#'   ggplot(aes(y = value,
#'              x = reorder(cohort, value, mean),
#'              fill = cohort)) + 
#'   geom_boxplot() +
#'   theme_RTCGA() +
#'   scale_fill_brewer(palette = "Set3") +
#'   facet_grid(mRNA~.) +
#'   theme(legend.position = "top")
#'
#'
#' ## RPPA expressions
#' library(RTCGA.RPPA)
#' expressionsTCGA(ACC.RPPA, BLCA.RPPA, BRCA.RPPA,
#'     extract.cols = c("4E-BP1_pS65", "4E-BP1")) %>%
#'   rename(cohort = dataset) %>%
#'   select(-bcr_patient_barcode) %>%
#'   gather(key = "RPPA", value = "value", -cohort)  %>%
#'   ggplot(aes(fill = cohort, 
#'              y = value,
#'              x = RPPA)) +
#'   geom_boxplot() +
#'   theme_dark(base_size = 15) +
#'   scale_fill_manual(values = c("#eb6420", "#207de5", "#fbca04")) +
#'   coord_flip() +
#'   theme(legend.position = "top") +
#'   geom_jitter(alpha = 0.5, col = "white", size = 0.6, width = 0.7)
#'
#'
#'
#' ## miRNASeq expressions 
#' library(RTCGA.miRNASeq)
#' # miRNASeq has bcr_patienct_barcode in rownames...
#' mutate(ACC.miRNASeq, 
#'    bcr_patient_barcode = substr(rownames(ACC.miRNASeq), 1, 25)) -> ACC.miRNASeq.bcr
#' mutate(CESC.miRNASeq, 
#'    bcr_patient_barcode = substr(rownames(CESC.miRNASeq), 1, 25)) -> CESC.miRNASeq.bcr
#' mutate(CHOL.miRNASeq, 
#'    bcr_patient_barcode = substr(rownames(CHOL.miRNASeq), 1, 25)) -> CHOL.miRNASeq.bcr
#' mutate(LAML.miRNASeq, 
#'    bcr_patient_barcode = substr(rownames(LAML.miRNASeq), 1, 25)) -> LAML.miRNASeq.bcr
#' mutate(PAAD.miRNASeq, 
#'    bcr_patient_barcode = substr(rownames(PAAD.miRNASeq), 1, 25)) -> PAAD.miRNASeq.bcr
#' mutate(THYM.miRNASeq, 
#'    bcr_patient_barcode = substr(rownames(THYM.miRNASeq), 1, 25)) -> THYM.miRNASeq.bcr
#' mutate(LGG.miRNASeq, 
#'    bcr_patient_barcode = substr(rownames(LGG.miRNASeq), 1, 25)) -> LGG.miRNASeq.bcr
#' mutate(STAD.miRNASeq, 
#'    bcr_patient_barcode = substr(rownames(STAD.miRNASeq), 1, 25)) -> STAD.miRNASeq.bcr
#' 
#' 
#' expressionsTCGA(ACC.miRNASeq.bcr, CESC.miRNASeq.bcr, CHOL.miRNASeq.bcr,
#'              LAML.miRNASeq.bcr, PAAD.miRNASeq.bcr, THYM.miRNASeq.bcr,
#'              LGG.miRNASeq.bcr, STAD.miRNASeq.bcr,
#'   extract.cols = c("machine", "hsa-mir-101-1", "miRNA_ID")) %>%
#'                 rename(cohort = dataset) %>%
#'    filter(miRNA_ID == "read_count") %>%
#'    select(-bcr_patient_barcode, -miRNA_ID) %>%
#'    gather(key = "key", value = "value", -cohort, -machine) %>%
#'    mutate(value = as.numeric(value)) %>%
#'    ggplot(aes(x = cohort,
#'               y = log1p(value),
#'               fill = as.factor(machine)) )+
#'    geom_boxplot() +
#'    theme_RTCGA(base_size = 13) +
#'    coord_flip() +
#'    theme(legend.position = "top") +
#'    scale_fill_brewer(palette = "Paired") +
#'    ggtitle("hsa-mir-101-1")
#' 
#' 
#' @family RTCGA
#' @rdname expressionsTCGA
#' @export
expressionsTCGA <- function(..., extract.cols = NULL, extract.names = TRUE) {
  assert_that(is.null(extract.cols) | is.character(extract.cols))
  assert_that(length(extract.names) == 1, is.logical(extract.names))
  
  
  dots <- list(...)
  lapply(dots, function(x){
    x <- x %>% purrr::map_if(is.factor, as.character)
  }) -> dots
  
  if (extract.names) {
    mapply(rep, 
           sapply(substitute(list(...))[-1], deparse), 
           lapply(list(...), nrow)) %>%  unlist %>% as.character -> dataset
    
    if(is.null(extract.cols)) {
      bind_rows(dots) %>%
        mutate(dataset = dataset) %>%
        select(everything())
    } else {
      bind_rows(dots) %>%
        mutate(dataset = dataset) %>%
        select(one_of(c("bcr_patient_barcode",
                        "dataset",
                        extract.cols)))
    }
  } else {
#     mapply(rep, 
#            sapply(substitute(list(...))[-1], deparse), 
#            lapply(list(...), nrow)) %>%  unlist -> dataset
    
    if(is.null(extract.cols)) {
      bind_rows(dots) %>%
#         mutate(dataset = dataset) %>%
        select(everything())
    } else {
      bind_rows(dots) %>%
    #    mutate(dataset = dataset) %>%
        select(one_of(c("bcr_patient_barcode",
                        "dataset",
                        extract.cols)))
    }
  }
}