R/olink_Pathway_Heatmap.R

In OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

#' Creates a heatmap of selected pathways and proteins
#'
#' Creates a heatmap of proteins related to pathways using enrichment results from olink_pathway_enrichment.
#'
#'@param enrich_results data frame of enrichment results from olink_pathway_enrichment()
#'@param test_results filtered results from statistical test with Assay, OlinkID, and estimate columns
#'@param method method used in olink_pathway_enrichment ("GSEA" (default) or "ORA")
#'@param keyword (optional) keyword to filter enrichment results on, if not specified, displays top terms
#'@param number_of_terms number of terms to display, default is 20
#'@return A heatmap as a ggplot object
#'@examples
#'\donttest{
#'library(dplyr)
#' # Run t-test results (see olink_ttest documentation)
#' npx_df <- npx_data1 %>% filter(!grepl('control',SampleID, ignore.case = TRUE))
#' ttest_results <- olink_ttest(df=npx_df,
#'                              variable = 'Treatment',
#'                             alternative = 'two.sided')
#'
#' try({ # This expression might fail if dependencies are not installed
#' #  Run olink_pathway_enrichment (see documentation)
#' gsea_results <- olink_pathway_enrichment(data = npx_data1, test_results = ttest_results)
#' ora_results <- olink_pathway_enrichment(data = npx_data1,
#'                                         test_results = ttest_results, method = "ORA")
#' olink_pathway_heatmap(enrich_results = gsea_results, test_results = ttest_results)
#' olink_pathway_heatmap(enrich_results = ora_results, test_results = ttest_results,
#'                       method = "ORA", keyword = "cell")
#' })
#'
#'
#'}
#'
#' @seealso \itemize{
#' \item{\code{\link[OlinkAnalyze:olink_pathway_enrichment]{olink_pathway_enrichment}} for generating enrichment results}
#' \item{\code{\link[OlinkAnalyze:olink_pathway_visualization]{olink_pathway_visualization}} for generating a bar graph of results}
#' }
#'@importFrom dplyr filter arrange slice_head desc inner_join
#'@importFrom ggplot2 ggplot aes geom_tile theme xlab ylab
#'@importFrom stringr str_trunc
#'@importFrom magrittr %>%
#'@export

olink_pathway_heatmap<- function(enrich_results, test_results, method = "GSEA", keyword = NULL, number_of_terms = 20) {
  if (!(method %in% c("ORA", "GSEA"))) {
    stop("Method must be \"GSEA\" or \"ORA\".")
  }

  if(!is.null(keyword)) {
    enrich_results <- enrich_results %>%
      dplyr::filter(grepl(pattern = toupper(keyword), x = Description))

    if (nrow(enrich_results) == 0) {
      stop("Keyword not found. Please choose a different keyword or use a set number of terms.")
    }
  }

  sub_enrich <- enrich_results %>%
    dplyr::arrange(pvalue) %>%
    dplyr::slice_head(n = number_of_terms) %>%
    dplyr::arrange(dplyr::desc(x = pvalue))

  if (method == "ORA"){
    results_list <- strsplit(x = sub_enrich$geneID, split = "/")
  } else if (method == "GSEA") {
    results_list <- strsplit(x = sub_enrich$core_enrichment, split = "/")
  }
  names(results_list) <- sub_enrich$Description

  long_list <- do.call(rbind, lapply(results_list, data.frame, stringsAsFactors = FALSE))
  long_list$Pathway <- row.names(long_list)
  long_list$Pathway <- gsub(pattern = "\\..*", replacement = "", x = long_list$Pathway)
  names(long_list)[1] <- "Assay"

  long_list1 <- long_list %>%
    as.data.frame() %>%
    dplyr::inner_join(test_results, by = "Assay") %>%
    dplyr::arrange(estimate)

  orderprot <- unique(long_list1$Assay)

  p <- ggplot2::ggplot(data = long_list1, ggplot2::aes(factor(x = Assay, levels = orderprot),
                                                       stringr::str_trunc(string = Pathway, width = 50, side = "center"))) +
    ggplot2::geom_tile(ggplot2::aes(fill = estimate)) +
    OlinkAnalyze::olink_fill_gradient(coloroption = c('teal', 'red'), name = "estimate") +
    OlinkAnalyze::set_plot_theme() +
    ggplot2::theme(panel.grid.major = ggplot2::element_blank(),
                   axis.text.x = ggplot2::element_text(angle = 60, hjust = 1)) +
    ggplot2::xlab("Protein Symbol") +
    ggplot2::ylab("Pathway")

  return(p)
}