heatmap_data_tables.R

In Emask7/ZIKVtranscriptomics: ZIKV Transcriptomics Analyses

library(dplyr)


get_heatmap_data <- function(search_term, DE_data, DAVID_data, file_name) {
  temp_colnames <- c("Gene_Symbol", colnames(DE_data))
  DE_data <- data.frame(rownames(DE_data), DE_data)
  colnames(DE_data) <- temp_colnames

  term_res <- subset(DAVID_data, DAVID_data$Term == search_term)

  if (nrow(term_res) == 0) return(data.frame())

  t3v0 <- data.frame(c(limma::strsplit2(term_res$Genes_t3v0, ", ")))
  colnames(t3v0) <- c("Gene_Symbol")

  t15v3 <- data.frame(c(limma::strsplit2(term_res$Genes_t15v3, ", ")))
  colnames(t15v3) <- c("Gene_Symbol")

  t15v0 <- data.frame(c(limma::strsplit2(term_res$Genes_t15v0, ", ")))
  colnames(t15v0) <- c("Gene_Symbol")

  all_genes <- dplyr::full_join(t3v0, t15v3)
  all_genes <- dplyr::full_join(all_genes, t15v0)
  all_genes <- subset(all_genes, !duplicated(all_genes[, 1]))

  res <- dplyr::left_join(all_genes, DE_data)
  res <- subset(res, !is.na(res[, 1]))

  if (!is.null(file_name)) {
    write.table(
      res, file = file_name, append = FALSE,
      sep = "\t", eol = "\n", quote = FALSE,
      row.names = FALSE, col.names = TRUE
    )
  }

  res
}



IFNab_sig_baboon <- get_heatmap_data(
  "R-HSA-909733",
  DESeq2_LRT_res_baboon, DAVID_results_baboon$Reactome$all,
  "IFN alpha beta signaling DE data - baboon alignment.txt"
)
head(IFNab_sig_baboon)


IFNab_sig_human <- get_heatmap_data(
  "R-HSA-909733",
  DESeq2_LRT_res_human, DAVID_results_human$Reactome$all,
  "IFN alpha beta signaling DE data - human alignment.txt"
)
head(IFNab_sig_human)

IFNg_sig_baboon <- get_heatmap_data(
  "R-HSA-877300",
  DESeq2_LRT_res_baboon, DAVID_results_baboon$Reactome$all,
  "IFN gamma signaling DE data - baboon alignment.txt"
)

IFNg_sig_human <- get_heatmap_data(
  "R-HSA-877300",
  DESeq2_LRT_res_human, DAVID_results_human$Reactome$all,
  "IFN gamma signaling DE data - human alignment.txt"
)




innate_imm_response_baboon <- get_heatmap_data(
  "innate immune response",
  DESeq2_LRT_res_baboon, DAVID_results_baboon$GO$all,
  "innate immune response DE data - baboon alignment.txt"
)

defense_response_to_virus_baboon <- get_heatmap_data(
  "defense response to virus",
  DESeq2_LRT_res_baboon, DAVID_results_baboon$GO$all,
  "defense response to virus DE data - baboon alignment.txt"
)

cytokine_sig_baboon <- get_heatmap_data(
  "cytokine-mediated signaling pathway",
  DESeq2_LRT_res_baboon, DAVID_results_baboon$GO$all,
  "cytokine-mediated signaling pathway DE data - baboon alignment.txt"
)

cytokine_sig_human <- get_heatmap_data(
  "cytokine-mediated signaling pathway",
  DESeq2_LRT_res_human, DAVID_results_human$GO$all,
  "cytokine-mediated signaling pathway DE data - human alignment.txt"
)

negative_reg_innate_imm_sys_process_baboon <- get_heatmap_data(
  "negative regulation of immune system process",
  DESeq2_LRT_res_baboon, DAVID_results_baboon$GO$all,
  "negative regulation of immune system process DE data - baboon alignment.txt"
)

positive_reg_innate_imm_sys_process_baboon <- get_heatmap_data(
  "positive regulation of immune system process",
  DESeq2_LRT_res_baboon, DAVID_results_baboon$GO$all,
  "positive regulation of immune system process DE data - baboon alignment.txt"
)

immune_response_baboon <- get_heatmap_data(
  "immune response",
  DESeq2_LRT_res_baboon, DAVID_results_baboon$GO$all,
  "Immune Response DE data - baboon alignment.txt"
)