fix plots for compound feature names

bigomics · Aug 9, 2024 · 6f801a7 · 6f801a7
1 parent 16e7fdb
commit 6f801a7
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Showing 3 changed files with 19 additions and 20 deletions.
diff --git a/components/board.dataview/R/dataview_plot_averagerank.R b/components/board.dataview/R/dataview_plot_averagerank.R
@@ -54,7 +54,8 @@ dataview_plot_averagerank_server <- function(id,
       nsamples <- length(samples)
 
       if (data_type %in% c("counts", "abundance")) {
-        mean.fc <- sort(rowMeans(pgx$counts[, samples, drop = FALSE], na.rm = TRUE), decreasing = TRUE)
+        mean.fc <- sort(rowMeans(pgx$counts[, samples, drop = FALSE], na.rm = TRUE),
+                        decreasing = TRUE)
         ylab <- tspan("Counts", js = FALSE)
       }
       if (data_type %in% c("logCPM", "log2")) {
@@ -155,7 +156,7 @@ dataview_plot_averagerank_server <- function(id,
         plotly::add_annotations(
           x = sel,
           y = mean.fc[sel],
-          ax = 20,
+          ax = ifelse(sel < length(mean.fc)/2, 40, -40),
           ay = -40,
           text = gene
         )

diff --git a/components/board.dataview/R/dataview_plot_correlation.R b/components/board.dataview/R/dataview_plot_correlation.R
@@ -39,9 +39,8 @@ dataview_plot_correlation_server <- function(id,
                                              r.samples = reactive(NULL),
                                              watermark = FALSE) {
   moduleServer(id, function(input, output, session) {
-    getTopCorrelatedGenes <- function(pgx, gene, n = 30, samples = NULL) {
-      samples <- r.samples()
-      gene <- r.gene()
+
+    getTopCorrelatedGenes <- function(pgx, gene, n, samples) {
 
       ## precompute
       if (is.null(samples)) samples <- colnames(pgx$X)
@@ -53,15 +52,15 @@ dataview_plot_correlation_server <- function(id,
       }
 
       samples <- intersect(samples, colnames(pgx$X))
-      pp <- rownames(pgx$genes)[match(gene, pgx$genes$gene_name)]
-
+      probe <- gene
+      
       ## corr always in log.scale and restricted to selected samples subset
       ## should match exactly the rawtable!!
-      if (pp %in% rownames(pgx$X)) {
-        rho <- cor(t(pgx$X[, samples]), pgx$X[pp, samples], use = "pairwise")[, 1]
-      } else if (pp %in% rownames(pgx$counts)) {
+      if (probe %in% rownames(pgx$X)) {
+        rho <- cor(t(pgx$X[, samples]), pgx$X[probe, samples], use = "pairwise")[, 1]
+      } else if (probe %in% rownames(pgx$counts)) {
         x0 <- playbase::logCPM(pgx$counts[, samples])
-        x1 <- x0[pp, ]
+        x1 <- x0[probe, ]
         rho <- cor(t(x0), x1, use = "pairwise")[, 1]
       } else {
         rho <- rep(0, nrow(pgx$genes))
@@ -175,7 +174,7 @@ dataview_plot_correlation_server <- function(id,
       df <- pd[[1]]
       df$genes <- factor(df$genes, levels = df$genes)
       df$gene_title <- stringr::str_extract(df$annot, "(?<=gene_title: <b>)[^<]+")
-      df$gene_name <- stringr::str_extract(df$annot, "(?<=gene_name: <b>)[^<]+")
+      df$gene_name  <- stringr::str_extract(df$annot, "(?<=gene_name: <b>)[^<]+")
       df$color <- NULL
       df$annot <- NULL
       return(df)

diff --git a/components/board.dataview/R/dataview_server.R b/components/board.dataview/R/dataview_server.R
@@ -284,9 +284,9 @@ DataViewBoard <- function(id, pgx) {
     ## ========================= FUNCTIONS ============================================
     ## ================================================================================
 
-    getCountStatistics <- reactiveVal()
-
-    observeEvent(
+##    getCountStatistics <- reactiveVal()
+##    observeEvent(
+    getCountStatistics <- eventReactive(
       {
         list(
           pgx$X,
@@ -327,7 +327,7 @@ DataViewBoard <- function(id, pgx) {
         colnames(counts) <- substring(colnames(counts), 1, 24)
 
         gset <- list()
-        gg <- pgx$genes[rownames(counts), ]$gene_name
+        gg <- pgx$genes[rownames(counts), ]$symbol
         tt <- pgx$genes[rownames(counts), ]$gene_title
         g1 <- gg[grep("^rpl|^rps", gg, ignore.case = TRUE)]
         g2 <- gg[grep("^mrpl|^mrps", gg, ignore.case = TRUE)]
@@ -389,10 +389,9 @@ DataViewBoard <- function(id, pgx) {
           prop.counts = prop.counts,
           gset.genes = gset.genes
         )
-        getCountStatistics(res)
-      },
-      ignoreNULL = TRUE
-    )
+        ##getCountStatistics(res)
+        return(res)
+      }, ignoreNULL = TRUE)
 
     ## ================================================================================
     ## ================================= END ====================================