fixed cusomized profile

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: PhyloProfile
-Version: 1.21.0
-Date: 2024-10-28
+Version: 1.21.1
+Date: 2024-11-01
 Title: PhyloProfile
 Authors@R: c(
     person("Vinh", "Tran", role = c("aut", "cre"), email = "[email protected]", comment=c(ORCID="0000-0001-6772-7595")),

R/umapClustering.R

@@ -256,14 +256,16 @@ createUmapPlotData <- function(
 #' Create UMAP cluster plot
 #' @export
 #' @usage plotUmap(plotDf = NULL, legendPos = "bottom", colorPalette = "Set2", 
-#'     transparent = 0, textSize = 12, font = "Arial", highlightTaxa = NULL)
+#'     transparent = 0, textSize = 12, font = "Arial", highlightTaxa = NULL,
+#'     dotZoom = 0)
 #' @param plotDf data for UMAP plot 
 #' @param legendPos position of legend. Default: "right"
 #' @param colorPalette color palette. Default: "Set2"
 #' @param transparent transparent level (from 0 to 1). Default: 0
 #' @param textSize size of axis and legend text. Default: 12
 #' @param font font of text. Default = Arial"
 #' @param highlightTaxa list of taxa to be highlighted
+#' @param dotZoom dot size zooming factor. Default: 0
 #' @return A plot as ggplot object
 #' @author Vinh Tran [email protected]
 #' @seealso \code{\link{prepareUmapData}}, \code{\link{umapClustering}},
@@ -280,7 +282,8 @@ createUmapPlotData <- function(
 
 plotUmap <- function(
     plotDf = NULL, legendPos = "bottom", colorPalette = "Set2", 
-    transparent = 0, textSize = 12, font = "Arial", highlightTaxa = NULL
+    transparent = 0, textSize = 12, font = "Arial", highlightTaxa = NULL,
+    dotZoom = 0
 ) {
     if (is.null(plotDf)) stop("Input data cannot be NULL!")
     X <- Y <- Label <- Freq <- NULL
@@ -302,13 +305,14 @@ plotUmap <- function(
         )
     }
     # adapt plot height based on number of labels
-    
+
     # generate plot
     plot <- ggplot(plotDf, aes(x = X, y = Y, color = Label)) +
         geom_point(aes(size = Freq), alpha = 1 - transparent) +
         geom_rug(alpha = 1) +
         theme_minimal() +
-        labs(x = "", y = "")
+        labs(x = "", y = "")+
+        scale_radius(range = c(1 + dotZoom, 6 + dotZoom))
     # change legend title
     if ("ncbiID" %in% colnames(plotDf)) {
         plot <- plot + guides(

inst/NEWS.Rd

@@ -2,6 +2,14 @@
 \title{PhyloProfile news}
 \encoding{UTF-8}
 
+\section{Version 1.20.1}{
+  \itemize{
+    \item auto identify refspec
+    \item fixed subsetting data using a list of gene IDs
+  }
+}
+
+
 \section{Version 1.20.0}{
   \itemize{
     \item added UMAP clustering

inst/PhyloProfile/R/createProfilePlot.R

@@ -133,7 +133,7 @@ createProfilePlot <- function(
             if (length(inSeq()) == 0 || length(inTaxa()) == 0) return()
             if ("all" %in% inSeq() & "all" %in% inTaxa()) return()
         }
-        if (mode() == "fast")
+        if (mode() == "fast" & typeProfile() != "customizedProfile")
             return(heatmapPlottingFast(dataHeat(), parameters()))
         return(heatmapPlotting(dataHeat(), parameters()))
     })
@@ -337,6 +337,9 @@ createProfilePlot <- function(
 
     # get info of clicked point on heatmap plot --------------------------------
     selectedpointInfo <- reactive({
+        req(dataHeat)
+        req(inSeq())
+        req(inTaxa())
         # get selected supertaxon name
         taxaList <- getNameList(taxDB())
         rankName <- rankSelect()
@@ -346,7 +349,7 @@ createProfilePlot <- function(
         if (mode() == "fast")
             dataHeat <- brushedData()
 
-        if (is.null(dataHeat)) {
+        if (is.null(dataHeat) | nrow(dataHeat) == 0) {
             message("WARNING: Data for heatmap is NULL!")
             return()
         }

inst/PhyloProfile/global.R

@@ -1,7 +1,7 @@
 #' Startup script for PhyloProfile
 #' 1) install and load packages
 #' 2) start the PhyloProfile app
-
+library(PhyloProfile)
 source("R/functions.R")
 
 # List of dependent packages --------------------------------------------------