fix columns

components/board.dataview/R/dataview_table_rawdata.R

@@ -139,44 +139,49 @@ dataview_table_rawdata_server <- function(id,
  }
 
  dbg("[dataview_rawdata:table_data] create dataframe")
- xgenes <- pgx$genes[rownames(x), "gene_name"]
- gene.title <- playdata::GENE_TITLE[toupper(xgenes)]
+ pp <- rownames(x)
+ feature <- pgx$genes[pp, "feature"]
+ symbol <- pgx$genes[pp, "symbol"] 
+ gene.title <- pgx$genes[pp, "gene_title"]
  gene.title <- substring(gene.title, 1, 50)
- if (is.null(rho)) {
- x <- data.frame(
- gene = xgenes, title = gene.title,
- AVG = avg,
- as.matrix(x), check.names = FALSE
- )
- } else {
- x <- data.frame(
- gene = xgenes, title = gene.title,
- rho = rho, SD = sdx, AVG = avg,
- as.matrix(x), check.names = FALSE
- )
+
+ df <- data.frame(
+ gene = feature,
+ symbol = symbol, 
+ title = gene.title,
+ rho = rho,
+ SD = sdx,
+ AVG = avg,
+ as.matrix(x),
+ check.names = FALSE
+ )
+
+ ## if symbol and feature as same, drop symbol column
+ if(mean(head(df$gene,1000)==head(df$symbol,1000)) > 0.8) {
+ df$symbol <- NULL
  }
- x <- x[order(-x$rho, -x$SD), , drop = FALSE]
 
  if (DATATYPEPGX == "proteomics") {
- colnames(x)[1] <- "protein"
+ colnames(df)[1] <- "protein"
  }
+ df <- df[order(-df$rho, -df$SD), , drop = FALSE]
 
  list(
- x = x,
+ df = df,
  x95 = x95,
  x99 = x99
  )
  })
 
  rawdataTable.RENDER <- function() {
  dt <- table_data()
- req(dt, dt$x)
+ req(dt, dt$df)
 
- numcols <- grep("gene|title", colnames(dt$x), value = TRUE, invert = TRUE)
+ numcols <- grep("gene|title", colnames(dt$df), value = TRUE, invert = TRUE)
  tabH <- 700 ## height of table
 
  DT::datatable(
- dt$x,
+ dt$df,
  rownames = FALSE,
  fillContainer = TRUE, #
  class = "compact hover",
@@ -204,7 +209,7 @@ dataview_table_rawdata_server <- function(id,
 
  rawdataTable.RENDER_modal <- shiny::reactive({
  dt <- rawdataTable.RENDER()
- dt$x$options$scrollY <- SCROLLY_MODAL
+ dt$df$options$scrollY <- SCROLLY_MODAL
  dt
  })