Merge pull request #38 from nuno-agostinho/dev

cTRAP 1.20.1

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: cTRAP
 Title: Identification of candidate causal perturbations from differential gene 
     expression data
-Version: 1.14.1
+Version: 1.20.1
 Authors@R: c(
         person(c("Bernardo", "P."), "de Almeida", role="aut"),
         person("Nuno", "Saraiva-Agostinho",
@@ -30,7 +30,7 @@ Suggests:
     spelling,
     biomaRt,
     remotes
-RoxygenNote: 7.2.0
+RoxygenNote: 7.3.1
 Imports: AnnotationDbi,
     AnnotationHub,
     binr,

NAMESPACE

@@ -67,7 +67,6 @@ importFrom(fastmatch,fmatch)
 importFrom(fgsea,calcGseaStat)
 importFrom(fgsea,fgsea)
 importFrom(ggplot2,aes)
-importFrom(ggplot2,aes_string)
 importFrom(ggplot2,annotate)
 importFrom(ggplot2,element_blank)
 importFrom(ggplot2,element_rect)

NEWS.md

@@ -1,3 +1,9 @@
+# cTRAP 1.20.1 (6 March, 2024)
+
+* When running `cTRAP()`, raise error if `commonPath` does not exist
+* Fix modular graphical interface functions not showing dropdown choices
+* Update icon names for FontAwesome 6
+
 # cTRAP 1.14.1 (14 July, 2022)
 
 * Add cTRAP version to welcome modal
@@ -145,7 +151,7 @@ down-regulated genes with `geneSize` argument:
 * Plotting:
     - `plot()` now supports plotting `predictTargetingDrugs()` results for a
     given drug, e.g. `plot(targetingDrugs, "1425")`
-    - `plot()` nows allows to set plot title with argument `title`
+    - `plot()` now allows to set plot title with argument `title`
     - `plot()` now plots results based on available methods instead of trying
     to plot based on results from `spearman` method only
     - GSEA plots now support two or less gene hits

R/drugSensitivity.R

@@ -734,7 +734,7 @@ plotTargetingDrug <- function(x, drug, method=c("spearman", "pearson", "gsea"),
         }
         df <- data.frame(input=input[intersecting], cor=val)
 
-        plot <- ggplot(df, aes_string("input", "cor")) +
+        plot <- ggplot(df, aes(.data[["input"]], .data[["cor"]])) +
             geom_point(alpha=0.1, na.rm=TRUE) +
             geom_rug(alpha=0.1) +
             geom_density_2d(na.rm=TRUE) +

R/plots.R

@@ -41,7 +41,7 @@ plotESplot <- function(enrichmentScore, gseaStat, compact=FALSE) {
         geom_hline(yintercept=0, colour="darkgrey", linetype="longdash") +
         geom_hline(yintercept=ES, colour="#3895D3") +
         geom_rug(alpha=rugAlpha, sides="b", length=unit(rugLength, "npc")) +
-        geom_line(colour="orange", na.rm=TRUE, size=0.7) +
+        geom_line(colour="orange", na.rm=TRUE, linewidth=0.7) +
         scale_x_continuous(expand=c(0,0)) +
         labs(y="Enrichment score") +
         theme_bw() +
@@ -94,14 +94,14 @@ plotMetricDistribution <- function(stat, compact=FALSE) {
     rankedMetric <- data.frame(sort=seq(stat), stat=stat, quantile=quantile)
 
     if (compact) {
-        aes        <- aes_string("sort", 0, fill="stat")
+        aes        <- aes(.data[["sort"]], 0, fill=.data[["stat"]])
         metricPlot <- ggplot(rankedMetric, aes) +
             geom_raster()
     } else {
-        aes        <- aes_string("sort", "stat")
+        aes        <- aes(.data[["sort"]], .data[["stat"]])
         metricPlot <- ggplot(rankedMetric, aes) +
-            geom_area(aes_string(group="quantile", fill="quantile"), na.rm=TRUE,
-                      position="identity")
+            geom_area(aes(group=.data[["quantile"]], fill=.data[["quantile"]]),
+                      na.rm=TRUE, position="identity")
     }
     xBreaks <- c(min(rankedMetric$sort),
                  extended_breaks()(rankedMetric$sort),
@@ -233,10 +233,11 @@ plotSingleCorr <- function(perturbation, ylabel, diffExprGenes, title=NULL) {
 
     multipleCellLines <- length(perturbation) > 1
     if (multipleCellLines) {
-        aesMap <- aes_string("diffExprGenes", "zscores", colour="perturbation")
+        aesMap <- aes(.data[["diffExprGenes"]], .data[["zscores"]],
+                      colour="perturbation")
         guide  <- guides(colour=guide_legend(title="Cell line"))
     } else {
-        aesMap <- aes_string("diffExprGenes", "zscores")
+        aesMap <- aes(.data[["diffExprGenes"]], .data[["zscores"]])
         guide  <- NULL
     }
 
@@ -378,7 +379,7 @@ plotComparison <- function(x, method, n, showMetadata,
     }
 
     # Correlation coefficient with labels for top and bottom perturbations
-    vars <- aes_string(x=1, y=stat, label="label", colour="ranked")
+    vars <- aes(x=1, y=.data[[stat]], label="label", colour="ranked")
     rug  <- geom_rug(alpha=alpha, sides="l")
 
     plot <- ggplot(x, vars) +
@@ -440,8 +441,8 @@ plotComparison <- function(x, method, n, showMetadata,
 #'
 #' @importFrom graphics plot
 #' @importFrom R.utils capitalize
-#' @importFrom ggplot2 ggplot aes_string geom_point geom_hline ylab theme
-#'   element_blank scale_colour_manual xlim theme_classic guides scale_y_reverse
+#' @importFrom ggplot2 ggplot aes geom_point geom_hline ylab theme element_blank
+#'   scale_colour_manual xlim theme_classic guides scale_y_reverse
 #' @importFrom ggrepel geom_text_repel
 #'
 #' @family functions related with the ranking of CMap perturbations
@@ -675,7 +676,7 @@ plotTargetingDrugsVSsimilarPerturbations <- function(
     ylabel <- paste("CMap comparison:", column)
     df$highlight <- highlight
 
-    plot <- ggplot(df, aes_string(cols[[1]], cols[[2]], colour=highlight)) +
+    plot <- ggplot(df, aes(.data[[ cols[[1]] ]], .data[[ cols[[2]] ]], colour=highlight)) +
         geom_point(alpha=0.7, show.legend=FALSE) +
         geom_rug(alpha=0.3, show.legend=FALSE) +
         xlab(xlabel) +

R/shinyInterface.R

@@ -109,7 +109,11 @@
 #' @keywords internal
 .prepareNavPage <- function(...) {
     app <- "cTRAP"
-    ui  <- navbarPage(app, ...) %>%
+    # Add JS and CSS in header
+    header <- tagList(
+        includeScript(system.file("shiny", "www", "cTRAP.js", package="cTRAP")),
+        includeCSS(system.file("shiny", "www", "cTRAP.css", package="cTRAP")))
+    ui  <- navbarPage(app, ..., header=header) %>%
         .replaceStrInList("navbar-static-top", "") %>%
         .replaceStrInList("container-fluid", "") %>%
         tags$div(class="container-fluid", style="padding-top: 15px;")
@@ -321,7 +325,7 @@
     diffExpr <- tags$span(
         "data-toggle"="tooltip", "data-placement"="right",
         title="Gene symbols and respective differential expression values (e.g. t-statistics)",
-        "Differential gene expression", icon("question-circle"))
+        "Differential gene expression", icon("circle-question"))
 
     sidebar <- sidebarPanel(
         textAreaInput(ns("diffExpr"), diffExpr, height="300px"),
@@ -1148,17 +1152,17 @@ convertTaskState2HTML <- function(state, toStr=TRUE, ..., label=FALSE) {
     state <- tolower(state)
     if (state %in% c("failure", "revoked")) {
         colour <- "red"
-        icon   <- icon("times-circle")
+        icon   <- icon("circle-xmark")
         state  <- "Error"
         class  <- "danger"
     } else if (state %in% c("not found")) {
         colour <- "red"
-        icon   <- icon("question-circle")
+        icon   <- icon("circle-question")
         state  <- "Not Found"
         class  <- "danger"
     } else if (state %in% c("received", "pending", "retry")) {
         colour <- "grey"
-        icon   <- icon("pause-circle")
+        icon   <- icon("circle-pause")
         state  <- "Waiting"
         class  <- "default"
     } else if (state %in% c("started")) {
@@ -1168,7 +1172,7 @@ convertTaskState2HTML <- function(state, toStr=TRUE, ..., label=FALSE) {
         class  <- "warning"
     } else if (state %in% c("success", "loaded")) {
         colour <- "green"
-        icon   <- icon("check-circle")
+        icon   <- icon("circle-check")
         state  <- "Loaded"
         class  <- "success"
     } else {
@@ -1711,7 +1715,7 @@ launchCMapDataLoader <- function(metadata="cmapMetadata.txt",
 #'
 #' @importFrom shiny runApp shinyApp
 #'
-#' @return Metadata viewer (retunrs \code{NULL})
+#' @return Metadata viewer (returns \code{NULL})
 #' @family visual interface functions
 #' @export
 launchMetadataViewer <- function(...) {

R/shinyInterface_session.R

@@ -63,12 +63,12 @@
     loadTokenUI <- tagList(
         textInput("token", "Insert token of a previous session:"),
         actionButton("loadToken", "Load session with token",
-                     width="100%", icon=icon("history"), class="btn-info"))
+                     width="100%", icon=icon("clock-rotate-left"), class="btn-info"))
     loadDataUI <- tagList(
         fileInput("sessionFile", width="100%", multiple=TRUE, accept=".rds",
                   "Upload RDS file of a previous session:"),
         actionButton("loadData", "Load session from RDS file", width="100%",
-                     icon=icon("history"), class="btn-info"))
+                     icon=icon("clock-rotate-left"), class="btn-info"))
     pills <- tabsetPanel(
         type="pills",
         tabPanel("Session token", loadTokenUI),
@@ -164,7 +164,7 @@ globalUI <- function(elems, idList, expire) {
                    .diffExprENCODEloaderUI(idList$encode),
                    "----",
                    .cmapDataLoaderUI(idList$cmap, globalUI=TRUE)),
-        navbarMenu("Analyse", icon=icon("cogs"),
+        navbarMenu("Analyse", icon=icon("gears"),
                    .rankSimilarPerturbationsUI(idList$rankPerts),
                    .predictTargetingDrugsUI(idList$predictDrugs)),
         navbarMenu("Visualise", icon=icon("chart-bar"),
@@ -178,12 +178,6 @@ globalUI <- function(elems, idList, expire) {
                    icon=icon("compass"), menuName="session"))
     ui <- .modifySessionUI(ui, expire=expire)
     ui <- .addLoadingStatus(ui)
-
-    # Add JS and CSS in header
-    header <- tags$head(
-        includeScript(system.file("shiny", "www", "cTRAP.js", package="cTRAP")),
-        includeCSS(system.file("shiny", "www", "cTRAP.css", package="cTRAP")))
-    ui <- tagList(header, ui)
     return(ui)
 }
 
@@ -439,6 +433,9 @@ updateAppData <- function(appData, x) {
 cTRAP <- function(..., commonPath="data", expire=14, fileSizeLimitMiB=50,
                   flowerURL=NULL, port=getOption("shiny.port"),
                   host=getOption("shiny.host", "127.0.0.1")) {
+    if (!dir.exists(commonPath)) {
+        stop("commonPath directory does not exist:", commonPath)
+    }
     .setFileSizeLimit(fileSizeLimitMiB)
     elems <- .prepareEllipsis(...)
 

dev/benchmark/R/memoryConsumptionPlot_help.R

@@ -78,8 +78,8 @@ addNAsBetweenCategories <- function(snap) {
 
 library(ggplot2)
 plotMemConsumption <- function(data) {
-  ggplot(data, aes_string("time / 60", "memory", ymax="memory",
-                          colour="category", fill="category")) +
+  ggplot(data, aes(.data[["time / 60"]], .data[["memory"]], ymax="memory",
+                   colour="category", fill="category")) +
     xlab("Time (minutes)") +
     ylab("Memory (GB)") +
     geom_ribbon(alpha=0.8, ymin=0) +

inst/WORDLIST

@@ -1,42 +1,61 @@
+API's
 Agostinho
+AnnotationHub
+BPPARAM
 Benjamini
 BiocViews
-biomaRt
-bplapply
-bpparam
-BPPARAM
 CMap
+CMap's
+COMPZ
 CTRP
+DT
+EIF
 ENSEMBL
+FontAwesome
 GCT
 GCTX
 GDSC
+GESA
+GSE
 GSEA
+HDF
+HepG
 Hochberg
+IPv
 ImmunoOncology
 Instituto
-knockdown
-Medicina
+LINCS
 MOA
+MODZ
+Medicina
+Minimial
 NCI
-nperm
-nproc
-pertubations
 RSEM
+RStudio
 Saraiva
-shRNA
-timepoint
-transcriptomic
+ShinyProxy
 Transcriptomics
-upregulation
 WTCS
+biomaRt
+bplapply
+bpparam
+dropdown
 filepath
-HepG
+floweRy
+gctx
+gseaParam
+gz
+knockdown
 nd
-CMap's
-EIF
-st
+negateive
+nperm
+nproc
+pos
 seq
-Minimial
+shRNA
+st
 statis
-gseaParam
+std
+timepoint
+transcriptomic
+upregulation

tests/testthat/test_plots.R

@@ -59,13 +59,12 @@ test_that("Plot similar perturbations with/without metadata", {
 test_that("Plot only ranked perturbations", {
     plot <- plot(cmp, "spearman", plotNonRankedPerturbations=FALSE)
     expect_s3_class(plot, "ggplot")
-    expect_equal(plot$guides$colour, "none")
+    expect_null(plot$guides$colour)
 })
 
 test_that("Plot non-ranked perturbations", {
     plot <- plot(cmp, "spearman", plotNonRankedPerturbations=TRUE)
     expect_s3_class(plot, "ggplot")
-    expect_identical(plot$labels$colour, "ranked")
     expect_null(plot$guides$colour)
 })