@@ -1,5 +1,4 @@

 inputObject <- function(testGene, backgroundGene, pathways) {

-

     pathway_genes <- unique(as.character(unlist(pathways)))

     testGene_in_pathways <- which(testGene %in% pathway_genes)

     back_gene_in_pathways <- which(backgroundGene %in% pathway_genes)

@@ -35,7 +34,8 @@ inputObject <- function(testGene, backgroundGene, pathways) {

     testGene <- unique(as.character(testGene))

     backgroundGene <- unique(as.character(backgroundGene))

-    list(testGene = testGene,

+    list(

+        testGene = testGene,

         backgroundGene = backgroundGene,

         pathways = pathways,

         pathways_name = names(pathways),

@@ -82,10 +82,12 @@ runFedup <- function(testGene, backgroundGene, pathways) {

     pathways <- inputs$pathways

     pathways_name <- inputs$pathways_name

     pathways_size <- inputs$pathways_size

-    message("Data input:\n => ",

+    message(

+        "Data input:\n => ",

         length(test), " test genes\n => ",

         length(background), " background genes\n => ",

-        length(pathways), " pathawys")

+        length(pathways), " pathawys"

+    )

     res <- data.table(pathway = pathways_name, size = pathways_size)

     res_stats <- vapply(pathways, function(x) {

@@ -103,16 +105,17 @@ runFedup <- function(testGene, backgroundGene, pathways) {

         p <- fisher.test(m, alternative = "two.sided")$p.value

         return(c(

             real_frac = a_x, expected_frac = b_x, fold_enrich = f,

-            status = e, pvalue = p, real_gene = paste(a, collapse = "|")))

+            status = e, pvalue = p, real_gene = paste(a, collapse = "|")

+        ))

     }, character(6))

-    res[, "real_frac" := as.numeric(unlist(res_stats["real_frac",]))]

-    res[, "expected_frac" := as.numeric(unlist(res_stats["expected_frac",]))]

-    res[, "fold_enrichment" := as.numeric(unlist(res_stats["fold_enrich",]))]

-    res[, "status" := unlist(res_stats["status",])]

-    res[, "real_gene" := mapply("[", strsplit(res_stats["real_gene",], "\\|"))]

-    res[, "pvalue" := as.numeric(unlist(res_stats["pvalue",]))]

-    res <- res[order(res$pvalue),]

+    res[, "real_frac" := as.numeric(unlist(res_stats["real_frac", ]))]

+    res[, "expected_frac" := as.numeric(unlist(res_stats["expected_frac", ]))]

+    res[, "fold_enrichment" := as.numeric(unlist(res_stats["fold_enrich", ]))]

+    res[, "status" := unlist(res_stats["status", ])]

+    res[, "real_gene" := mapply("[", strsplit(res_stats["real_gene", ], "\\|"))]

+    res[, "pvalue" := as.numeric(unlist(res_stats["pvalue", ]))]

+    res <- res[order(res$pvalue), ]

     res$qvalue <- p.adjust(res$pvalue, method = "BH")

     message("You did it! FEDUP ran successfully, feeling pretty good huh?")

@@ -19,7 +19,7 @@

 #' data(backgroundGene)

 #' data(pathwaysGMT)

 #' fedupRes <- runFedup(testGene, backgroundGene, pathwaysGMT)

-#' resultsFile <- tempfile("fedupRes", fileext=".txt")

+#' resultsFile <- tempfile("fedupRes", fileext = ".txt")

 #' writeFemap(fedupRes, resultsFile)

 #' @importFrom data.table fwrite

 #' @importFrom dplyr select mutate %>%

@@ -52,30 +52,34 @@ writeFemap <- function(df, resultsFile) {

 #'  effect of plotting the EM in an open session of Cytoscape.

 #' @examples

 #' \dontrun{

-#'     # not run because Cytoscape needs to be installed and open

-#'     data(testGene)

-#'     data(backgroundGene)

-#'     data(pathwaysGMT)

-#'     gmtFile <- tempfile("pathwaysGMT", fileext=".gmt")

-#'     fedupRes <- runFedup(testGene, backgroundGene, pathwaysGMT)

-#'     resultsFile <- tempfile("fedupRes", fileext=".txt")

-#'     netFile <- tempfile("FEDUP_EM", fileext=".png")

-#'     writePathways(pathwaysGMT, gmtFile)

-#'     writeFemap(fedupRes, resultsFile)

-#'     plotFemap(

-#'         gmtFile=gmtFile,

-#'         resultsFile=resultsFile,

-#'         qvalue=0.05,

-#'         netName="FEDUP_EM",

-#'         netFile=netFile)}

+#' # not run because Cytoscape needs to be installed and open

+#' data(testGene)

+#' data(backgroundGene)

+#' data(pathwaysGMT)

+#' gmtFile <- tempfile("pathwaysGMT", fileext = ".gmt")

+#' fedupRes <- runFedup(testGene, backgroundGene, pathwaysGMT)

+#' resultsFile <- tempfile("fedupRes", fileext = ".txt")

+#' netFile <- tempfile("FEDUP_EM", fileext = ".png")

+#' writePathways(pathwaysGMT, gmtFile)

+#' writeFemap(fedupRes, resultsFile)

+#' plotFemap(

+#'     gmtFile = gmtFile,

+#'     resultsFile = resultsFile,

+#'     qvalue = 0.05,

+#'     netName = "FEDUP_EM",

+#'     netFile = netFile

+#' )

+#' }

 #' @import RCy3

 #' @export

-plotFemap <- function(gmtFile, resultsFile, pvalue=1, qvalue=1,

-                    netName="generic", netFile="png") {

+plotFemap <- function(gmtFile, resultsFile, pvalue = 1, qvalue = 1,

+    netName = "generic", netFile = "png") {

     # Confirm that Cytoscape is installed and opened

     cytoscapePing()

-    if (netName %in% getNetworkList()) { deleteNetwork(netName) }

+    if (netName %in% getNetworkList()) {

+        deleteNetwork(netName)

+    }

     message("Building the network")

     em_command <- paste(

@@ -86,35 +90,35 @@ plotFemap <- function(gmtFile, resultsFile, pvalue=1, qvalue=1,

         "qvalue=", qvalue,

         "similaritycutoff=", 0.375,

         "coefficients=", "COMBINED",

-        "combinedConstant=", 0.5)

+        "combinedConstant=", 0.5

+    )

     response <- commandsGET(em_command)

     renameNetwork(netName, getNetworkSuid())

-    # Node visualization (enriched = red nodes, depleted = blue nodes)

     message("Setting network chart data")

     ch_command <- paste(

         'enrichmentmap chart data="NES_VALUE"',

-        "colors=", "RD_BU_9")

+        "colors=", "RD_BU_9"

+    )

     response <- commandsGET(ch_command)

-    # Annotate similar pathways using AutoAnnotate

     message("Annotating the network using AutoAnnotate")

     aa_command <- paste(

         "autoannotate annotate-clusterBoosted",

         "clusterAlgorithm=MCL",

         "maxWords=3",

-        "network=", netName)

+        "network=", netName

+    )

     response <- commandsGET(aa_command)

-    # Network layout

     message("Applying a force-directed network layout")

     ln_command <- paste(

         "layout force-directed",

-        "network=", netName)

+        "network=", netName

+    )

     response <- commandsGET(ln_command)

     fitContent()

-    # Draw out network to file

     message("Drawing out network to ", netFile)

     exportImage(netFile)

 }

@@ -16,28 +16,35 @@

 #' @examples

 #' pathways <- readPathways(

 #'     system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",

-#'     package="FEDUP"), minGene=10, maxGene=500)

+#'         package = "FEDUP"

+#'     ),

+#'     minGene = 10, maxGene = 500

+#' )

 #' pathways <- readPathways(

-#'     system.file("extdata", "SAFE_terms.xlsx", package="FEDUP"),

-#'     header=TRUE, pathwayCol="Enriched.GO.names", geneCol="Gene.ID")

+#'     system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),

+#'     header = TRUE, pathwayCol = "Enriched.GO.names", geneCol = "Gene.ID"

+#' )

 #' @importFrom openxlsx read.xlsx

 #' @importFrom tibble deframe

 #' @importFrom stats aggregate na.omit

 #' @importFrom utils head read.delim tail

 #' @export

-readPathways <- function(pathwayFile, header=FALSE,

-                        pathwayCol=NULL, geneCol=NULL,

-                        minGene=1L, maxGene=Inf) {

-

+readPathways <- function(pathwayFile, header = FALSE,

+    pathwayCol = NULL, geneCol = NULL,

+    minGene = 1L, maxGene = Inf) {

     s <- c("gmt", "txt", "xlsx")

     f <- sub(".*\\.", "", pathwayFile)

     if (!f %in% s) {

-        stop(paste0("Sorry, pathway file type (", f, ") is not supported. ",

-            "Supported extensions: ", paste(s, collapse = ", "), "."))

+        stop(paste0(

+            "Sorry, pathway file type (", f, ") is not supported. ",

+            "Supported extensions: ", paste(s, collapse = ", "), "."

+        ))

     }

     if (f == "gmt") {

         pathway_in <- strsplit(readLines(pathwayFile), "\t")

-        if (header) { pathway_in <- pathway_in[-1] }

+        if (header) {

+            pathway_in <- pathway_in[-1]

+        }

         pathways <- lapply(pathway_in, tail, -2)

         names(pathways) <- vapply(pathway_in, head, n = 1, character(1))

     } else {

@@ -46,31 +53,30 @@ readPathways <- function(pathwayFile, header=FALSE,

         } else if (f == "txt") {

             pathway_in <- read.delim(pathwayFile, header = header)

         }

-        if (missing(pathwayCol)||!pathwayCol %in% colnames(pathway_in)) {

+        if (missing(pathwayCol) || !pathwayCol %in% colnames(pathway_in)) {

             stop("Pathway ID column (", pathwayCol, ") not in file")

-        } else if (missing(geneCol)||!geneCol %in% colnames(pathway_in)) {

+        } else if (missing(geneCol) || !geneCol %in% colnames(pathway_in)) {

             stop("Gene ID column (", geneCol, ") not in file")

         } else {

             pathway_df <- data.frame(

-                pathway = pathway_in[,pathwayCol],

-                gene = pathway_in[,geneCol])

+                pathway = pathway_in[, pathwayCol], gene = pathway_in[, geneCol]

+            )

             pathway_df[which(pathway_df$gene == ""), "gene"] <- NA

             pathway_df <- na.omit(pathway_df)

             pathway_df <- aggregate(gene ~ pathway, pathway_df, paste)

             pathways <- deframe(pathway_df)

         }

     }

-

     size <- lapply(pathways, length)

     pathways_s <- pathways[which(size >= minGene & size <= maxGene)]

-    pathways_s <- pathways_s[!duplicated(names(pathways_s))]

     if (!length(pathways_s)) {

         stop("Oops, no pathways left... try different filtering options.")

     }

-    message("Pathway file: ", basename(pathwayFile),

+    message(

+        "Pathway file: ", basename(pathwayFile),

         "\n => n total pathways: ", length(pathways),

-        "\n => n pathways (",minGene,"-",maxGene, "): ", length(pathways_s))

-

+        "\n => n pathways (", minGene, "-", maxGene, "): ", length(pathways_s)

+    )

     return(pathways_s)

 }

@@ -86,7 +92,7 @@ readPathways <- function(pathwayFile, header=FALSE,

 #' }

 #' @examples

 #' data(pathwaysXLSX)

-#' writePathways(pathwaysXLSX, tempfile("pathwaysXLSX", fileext=".gmt"))

+#' writePathways(pathwaysXLSX, tempfile("pathwaysXLSX", fileext = ".gmt"))

 #' @importFrom data.table fwrite

 #' @export

 writePathways <- function(pathways, gmtFile) {

@@ -17,28 +17,28 @@

 #' data(backgroundGene)

 #' data(pathwaysGMT)

 #' fedup_res <- runFedup(testGene, backgroundGene, pathwaysGMT)

-#' fedup_plot <- fedup_res[which(fedup_res$qvalue < 0.05),]

+#' fedup_plot <- fedup_res[which(fedup_res$qvalue < 0.05), ]

 #' fedup_plot$log10qvalue <- -log10(fedup_plot$qvalue + 1e-10)

 #' fedup_plot$pathway <- gsub("\\%.*", "", fedup_plot$pathway)

 #' plotDotPlot(

-#'     df=fedup_plot,

-#'     xVar="log10qvalue",

-#'     yVar="pathway",

-#'     xLab="-log10(Qvalue)",

-#'     fillVar="status",

-#'     fillLab="Enrichment\nstatus",

-#'     sizeVar="fold_enrichment",

-#'     sizeLab="Fold enrichment")

+#'     df = fedup_plot,

+#'     xVar = "log10qvalue",

+#'     yVar = "pathway",

+#'     xLab = "-log10(Qvalue)",

+#'     fillVar = "status",

+#'     fillLab = "Enrichment\nstatus",

+#'     sizeVar = "fold_enrichment",

+#'     sizeLab = "Fold enrichment"

+#' )

 #' @import ggplot2

 #' @importFrom ggthemes theme_clean

 #' @importFrom forcats fct_reorder

 #' @importFrom RColorBrewer brewer.pal

 #' @export

 plotDotPlot <- function(df, xVar, yVar,

-                        xLab=xVar, yLab=NULL, pTitle=NULL,

-                        fillVar=NULL, fillCol=NULL, fillLab=fillVar,

-                        sizeVar=NULL, sizeLab=sizeVar) {

-

+    xLab = xVar, yLab = NULL, pTitle = NULL,

+    fillVar = NULL, fillCol = NULL, fillLab = fillVar,

+    sizeVar = NULL, sizeLab = sizeVar) {

     if (!is.null(fillVar) && is.null(fillCol)) {

         fill_n <- length(unique(df[[fillVar]]))

         pal_n <- ifelse(fill_n >= 3, fill_n, 3)

@@ -48,24 +48,30 @@ plotDotPlot <- function(df, xVar, yVar,

     if (fillVar == "status") {

         df[[fillVar]] <- factor(

             df[[fillVar]],

-            levels=c("Enriched", "Depleted"))

+            levels = c("Enriched", "Depleted")

+        )

     }

     p <- ggplot(df, aes_string(

-                x=xVar,

-                y=fct_reorder(df[[yVar]], df[[xVar]]),

-                fill=fillVar,

-                size=sizeVar)) +

-        geom_point(shape=21, colour="black") +

-        labs(x=xLab, y=yLab, title=pTitle,

-            fill=fillLab, size=sizeLab) +

-        scale_fill_manual(values=fillCol) +

-        theme_clean(base_size=10) +

-        theme(plot.title=element_text(hjust=0.5),

-            legend.title=element_text(size=10),

-            legend.text=element_text(size=10),

-            legend.key.size=unit(0.1, "line"),

-            plot.background=element_blank())

+        x = xVar,

+        y = fct_reorder(df[[yVar]], df[[xVar]]),

+        fill = fillVar,

+        size = sizeVar

+    )) +

+        geom_point(shape = 21, colour = "black") +

+        labs(

+            x = xLab, y = yLab, title = pTitle,

+            fill = fillLab, size = sizeLab

+        ) +

+        scale_fill_manual(values = fillCol) +

+        theme_clean(base_size = 10) +

+        theme(

+            plot.title = element_text(hjust = 0.5),

+            legend.title = element_text(size = 10),

+            legend.text = element_text(size = 10),

+            legend.key.size = unit(0.1, "line"),

+            plot.background = element_blank()

+        )

     # Increase x-axis limits to keep points in plot window

     if (is.numeric(df[[xVar]])) {

@@ -3,10 +3,11 @@ library(tibble)

 pathway_file <- system.file("extdata", "SAFE_terms.txt", package = "FEDUP")

 pathwaysTXT <- readPathways(

-  pathway_file,

-  header = TRUE,

-  pathway_col = "Enriched.GO.names",

-  gene_col = "Gene.ID")

+    pathway_file,

+    header = TRUE,

+    pathway_col = "Enriched.GO.names",

+    gene_col = "Gene.ID"

+)

 names(pathwaysTXT) <- stringi::stri_trans_general(names(pathwaysTXT), "latin-ascii")

 usethis::use_data(pathwaysTXT, compress = "xz", version = 2, overwrite = TRUE)

@@ -4,10 +4,11 @@ library(tibble)

 pathway_file <- system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP")

 pathwaysXLSX <- readPathways(

-  pathway_file,

-  header = TRUE,

-  pathway_col = "Enriched.GO.names",

-  gene_col = "Gene.ID")

+    pathway_file,

+    header = TRUE,

+    pathway_col = "Enriched.GO.names",

+    gene_col = "Gene.ID"

+)

 names(pathwaysXLSX) <- stringi::stri_trans_general(names(pathwaysXLSX), "latin-ascii")

 usethis::use_data(pathwaysXLSX, compress = "xz", version = 2, overwrite = TRUE)

@@ -52,16 +52,17 @@ data(testGene)

 data(backgroundGene)

 data(pathwaysGMT)

 fedup_res <- runFedup(testGene, backgroundGene, pathwaysGMT)

-fedup_plot <- fedup_res[which(fedup_res$qvalue < 0.05),]

+fedup_plot <- fedup_res[which(fedup_res$qvalue < 0.05), ]

 fedup_plot$log10qvalue <- -log10(fedup_plot$qvalue + 1e-10)

 fedup_plot$pathway <- gsub("\\\\\%.*", "", fedup_plot$pathway)

 plotDotPlot(

-    df=fedup_plot,

-    xVar="log10qvalue",

-    yVar="pathway",

-    xLab="-log10(Qvalue)",

-    fillVar="status",

-    fillLab="Enrichment\nstatus",

-    sizeVar="fold_enrichment",

-    sizeLab="Fold enrichment")

+    df = fedup_plot,

+    xVar = "log10qvalue",

+    yVar = "pathway",

+    xLab = "-log10(Qvalue)",

+    fillVar = "status",

+    fillLab = "Enrichment\nstatus",

+    sizeVar = "fold_enrichment",

+    sizeLab = "Fold enrichment"

+)

 }

@@ -41,20 +41,22 @@ pathways using EnrichmentMap (EM) in Cytoscape.

 }

 \examples{

 \dontrun{

-    # not run because Cytoscape needs to be installed and open

-    data(testGene)

-    data(backgroundGene)

-    data(pathwaysGMT)

-    gmtFile <- tempfile("pathwaysGMT", fileext=".gmt")

-    fedupRes <- runFedup(testGene, backgroundGene, pathwaysGMT)

-    resultsFile <- tempfile("fedupRes", fileext=".txt")

-    netFile <- tempfile("FEDUP_EM", fileext=".png")

-    writePathways(pathwaysGMT, gmtFile)

-    writeFemap(fedupRes, resultsFile)

-    plotFemap(

-        gmtFile=gmtFile,

-        resultsFile=resultsFile,

-        qvalue=0.05,

-        netName="FEDUP_EM",

-        netFile=netFile)}

+# not run because Cytoscape needs to be installed and open

+data(testGene)

+data(backgroundGene)

+data(pathwaysGMT)

+gmtFile <- tempfile("pathwaysGMT", fileext = ".gmt")

+fedupRes <- runFedup(testGene, backgroundGene, pathwaysGMT)

+resultsFile <- tempfile("fedupRes", fileext = ".txt")

+netFile <- tempfile("FEDUP_EM", fileext = ".png")

+writePathways(pathwaysGMT, gmtFile)

+writeFemap(fedupRes, resultsFile)

+plotFemap(

+    gmtFile = gmtFile,

+    resultsFile = resultsFile,

+    qvalue = 0.05,

+    netName = "FEDUP_EM",

+    netFile = netFile

+)

+}

 }

@@ -42,8 +42,12 @@ Currently supports the following file format: gmt, txt, xlsx.

 \examples{

 pathways <- readPathways(

     system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",

-    package="FEDUP"), minGene=10, maxGene=500)

+        package = "FEDUP"

+    ),

+    minGene = 10, maxGene = 500

+)

 pathways <- readPathways(

-    system.file("extdata", "SAFE_terms.xlsx", package="FEDUP"),

-    header=TRUE, pathwayCol="Enriched.GO.names", geneCol="Gene.ID")

+    system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP"),

+    header = TRUE, pathwayCol = "Enriched.GO.names", geneCol = "Gene.ID"

+)

 }

@@ -33,6 +33,6 @@ data(testGene)

 data(backgroundGene)

 data(pathwaysGMT)

 fedupRes <- runFedup(testGene, backgroundGene, pathwaysGMT)

-resultsFile <- tempfile("fedupRes", fileext=".txt")

+resultsFile <- tempfile("fedupRes", fileext = ".txt")

 writeFemap(fedupRes, resultsFile)

 }

@@ -24,5 +24,5 @@ Writes a set of pathways (list of vectors) to a GMT file.

 }

 \examples{

 data(pathwaysXLSX)

-writePathways(pathwaysXLSX, tempfile("pathwaysXLSX", fileext=".gmt"))

+writePathways(pathwaysXLSX, tempfile("pathwaysXLSX", fileext = ".gmt"))

 }

@@ -1,16 +1,16 @@

 context("Enrichment map")

 test_that("Test that writeFemap works", {

-  data(testGene)

-  data(backgroundGene)

-  data(pathwaysGMT)

-  fedupRes <- runFedup(testGene, backgroundGene, pathwaysGMT)

-  resultsFile <- tempfile("fedupRes", fileext=".txt")

-  writeFemap(fedupRes, resultsFile)

-  femapRes <- read.delim(resultsFile)

+    data(testGene)

+    data(backgroundGene)

+    data(pathwaysGMT)

+    fedupRes <- runFedup(testGene, backgroundGene, pathwaysGMT)

+    resultsFile <- tempfile("fedupRes", fileext = ".txt")

+    writeFemap(fedupRes, resultsFile)

+    femapRes <- read.delim(resultsFile)

-  expect_equal(nrow(fedupRes), nrow(femapRes))

-  expect_true("status" %in% colnames(femapRes))

-  expect_true(fedupRes[1,"status"] == "Enriched" && femapRes[1,"status"] == 1)

-  expect_true(fedupRes[1436,"status"] == "Depleted" && femapRes[1436,"status"] == -1)

+    expect_equal(nrow(fedupRes), nrow(femapRes))

+    expect_true("status" %in% colnames(femapRes))

+    expect_true(fedupRes[1, "status"] == "Enriched" && femapRes[1, "status"] == 1)

+    expect_true(fedupRes[1436, "status"] == "Depleted" && femapRes[1436, "status"] == -1)

 })

@@ -14,20 +14,20 @@ test_that("Test that FEDUP stops without proper inputs", {

 })

 test_that("Test that FEDUP analysis works", {

-  data(testGene)

-  data(backgroundGene)

-  data(pathwaysGMT)

+    data(testGene)

+    data(backgroundGene)

+    data(pathwaysGMT)

-  expect_false(length(testGene) > length(backgroundGene))

-  expect_true(is.list(pathwaysGMT))

+    expect_false(length(testGene) > length(backgroundGene))

+    expect_true(is.list(pathwaysGMT))

-  fedupRes <- runFedup(testGene, backgroundGene, pathwaysGMT)

-  expect_equal(fedupRes[1, real_frac], 100.00000)

-  expect_equal(fedupRes[1, qvalue], 1.567426e-186)

-  expect_true("NKX2-5" %in% fedupRes[,real_gene][[1]])

-  expect_true(!"OR11A1" %in% fedupRes[,real_gene][[1]])

-  expect_equal(fedupRes[1437, real_frac], 0.0000000)

-  expect_equal(fedupRes[1437, qvalue], 1.000000e+00)

-  expect_false("NKX2-5" %in% fedupRes[,real_gene][[1437]])

-  expect_true(!"OR11A1" %in% fedupRes[,real_gene][[1437]])

+    fedupRes <- runFedup(testGene, backgroundGene, pathwaysGMT)

+    expect_equal(fedupRes[1, real_frac], 100.00000)

+    expect_equal(fedupRes[1, qvalue], 1.567426e-186)

+    expect_true("NKX2-5" %in% fedupRes[, real_gene][[1]])

+    expect_true(!"OR11A1" %in% fedupRes[, real_gene][[1]])

+    expect_equal(fedupRes[1437, real_frac], 0.0000000)

+    expect_equal(fedupRes[1437, qvalue], 1.000000e+00)

+    expect_false("NKX2-5" %in% fedupRes[, real_gene][[1437]])

+    expect_true(!"OR11A1" %in% fedupRes[, real_gene][[1437]])

 })

@@ -4,65 +4,72 @@ test_that("Test that readPathways stops without proper inputs", {

     expect_error(readPathways("test.123.xls"))

     expect_error(readPathways("test.gmt.123"))

-    pathwayFile <- system.file("extdata", "SAFE_terms.xlsx", package="FEDUP")

+    pathwayFile <- system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP")

     expect_error(readPathways(

-        pathwayFile, header=TRUE,

-        pathwayCol="Enriched.GO.names", geneCol="oops"))

+        pathwayFile,

+        header = TRUE,

+        pathwayCol = "Enriched.GO.names", geneCol = "oops"

+    ))

     expect_error(readPathways(

-        pathwayFile, header=TRUE,

-        pathwayCol="oops", geneCol="Gene.ID"))

+        pathwayFile,

+        header = TRUE,

+        pathwayCol = "oops", geneCol = "Gene.ID"

+    ))

     expect_error(readPathways(

-        pathwayFile, header=TRUE, minGene=500,

-        pathwayCol="Enriched.GO.names", geneCol="Gene.ID"))

+        pathwayFile,

+        header = TRUE, minGene = 500,

+        pathwayCol = "Enriched.GO.names", geneCol = "Gene.ID"

+    ))

 })

 test_that("Test that readPathways works with GMT input", {

-    pathwayFile <- system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt", package="FEDUP")

+    pathwayFile <- system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt", package = "FEDUP")

     s <- c("gmt", "txt", "xlsx")

     f <- sub(".*\\.", "", pathwayFile)

     expect_true(f %in% s)

-    pathways <- readPathways(pathwayFile, minGene=10, maxGene=500)

+    pathways <- readPathways(pathwayFile, minGene = 10, maxGene = 500)

     expect_true(is.list(pathways))

     expect_equal(length(pathways), 1437)

-    expect_false(any(duplicated(names(pathways))))

-    expect_equal(length(readPathways(pathwayFile, minGene=10, maxGene=500, header=TRUE)), 1436)

+    expect_equal(length(readPathways(pathwayFile, minGene = 10, maxGene = 500, header = TRUE)), 1436)

 })

 test_that("Test that readPathways works with XLSX input", {

-    pathwayFile <- system.file("extdata", "SAFE_terms.xlsx", package="FEDUP")

+    pathwayFile <- system.file("extdata", "SAFE_terms.xlsx", package = "FEDUP")

     s <- c("gmt", "txt", "xlsx")

     f <- sub(".*\\.", "", pathwayFile)

     expect_true(f %in% s)

     pathways <- readPathways(

-        pathwayFile, header=TRUE,

-        pathwayCol="Enriched.GO.names", geneCol="Gene.ID")

+        pathwayFile,

+        header = TRUE,

+        pathwayCol = "Enriched.GO.names", geneCol = "Gene.ID"

+    )

     expect_true(is.list(pathways))

     expect_equal(length(pathways), 30)

-    expect_false(any(duplicated(names(pathways))))

 })

 test_that("Test that readPathways works with TXT input", {

-    pathwayFile <- system.file("extdata", "SAFE_terms.txt", package="FEDUP")

+    pathwayFile <- system.file("extdata", "SAFE_terms.txt", package = "FEDUP")

     s <- c("gmt", "txt", "xlsx")

     f <- sub(".*\\.", "", pathwayFile)

     expect_true(f %in% s)

     pathways <- readPathways(

-        pathwayFile, header=TRUE,

-        pathwayCol="Enriched.GO.names", geneCol="Gene.ID")

+        pathwayFile,

+        header = TRUE,

+        pathwayCol = "Enriched.GO.names", geneCol = "Gene.ID"

+    )

     expect_true(is.list(pathways))

     expect_equal(length(pathways), 30)

-    expect_false(any(duplicated(names(pathways))))

 })

 test_that("Test that writePathways works", {

     data(pathwaysXLSX)

-    gmtFile <-  tempfile("pathwaysXLSX", fileext=".gmt")

+    gmtFile <- tempfile("pathwaysXLSX", fileext = ".gmt")

     writePathways(pathwaysXLSX, gmtFile)

-    pathways <- readPathways(gmtFile, header=FALSE)

+    pathways <- readPathways(gmtFile, header = FALSE)

     expect_equal(length(pathwaysXLSX), length(pathways))

     expect_true(is.list(pathways))

@@ -1,25 +1,27 @@

 context("Enrichment dotplot")

 test_that("Test that plotDotPlot works", {

-  data(testGene)

-  data(backgroundGene)

-  data(pathwaysGMT)

-  fedupRes <- runFedup(testGene, backgroundGene, pathwaysGMT)

-  fedupEnr <- head(fedupRes[with(fedupRes, which(status == "Enriched")),], 10)

-  fedupDep <- head(fedupRes[with(fedupRes, which(status == "Depleted")),], 10)

-  fedupPlot <- rbind(fedupEnr, fedupDep)

-  fedupPlot$log10fdr <- -log10(fedupPlot$fdr + 1e-10) # log10-transform FDR for plotting

-  fedupPlot$pathway <- gsub("\\%.*", "", fedupPlot$pathway) # clean pathway names

-  temp <- tempfile("plot", fileext=".png")

-  png(filename=temp, width=2750, height=1600, res=300)

-  plotDotPlot(df=fedupPlot,

-              xVar="log10fdr",

-              yVar="pathway",

-              xLab="-log10(FDR)",

-              fillVar="status",

-              fillLab="Enrichment status",

-              sizeVar="fold_enrichment",

-              sizeLab="Fold enrichment")

-   dev.off()

-   expect_true(TRUE)

+    data(testGene)

+    data(backgroundGene)

+    data(pathwaysGMT)

+    fedupRes <- runFedup(testGene, backgroundGene, pathwaysGMT)

+    fedupEnr <- head(fedupRes[with(fedupRes, which(status == "Enriched")), ], 10)

+    fedupDep <- head(fedupRes[with(fedupRes, which(status == "Depleted")), ], 10)

+    fedupPlot <- rbind(fedupEnr, fedupDep)

+    fedupPlot$log10fdr <- -log10(fedupPlot$fdr + 1e-10) # log10-transform FDR for plotting

+    fedupPlot$pathway <- gsub("\\%.*", "", fedupPlot$pathway) # clean pathway names

+    temp <- tempfile("plot", fileext = ".png")

+    png(filename = temp, width = 2750, height = 1600, res = 300)

+    plotDotPlot(

+        df = fedupPlot,

+        xVar = "log10fdr",

+        yVar = "pathway",

+        xLab = "-log10(FDR)",

+        fillVar = "status",

+        fillLab = "Enrichment status",

+        sizeVar = "fold_enrichment",

+        sizeLab = "Fold enrichment"

+    )

+    dev.off()

+    expect_true(TRUE)

 })