@@ -6,9 +6,9 @@

 #'

 #' Raw data location

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

-#'     package = "FEDUP")

+#'     package="FEDUP")

 #' Script to prepare data

-#' system.file("data-raw", "pathwaysGMT.R", package = "FEDUP")

+#' system.file("data-raw", "pathwaysGMT.R", package="FEDUP")

 #'

 #' @format a named list of 1437 vectors

 "pathwaysGMT"

@@ -16,10 +16,10 @@

 #' Example list of yeast SAFE terms obtained from a XLSX file.

 #'

 #' Raw data location

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

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

 #'

 #' Script to prepare data

-#' system.file("data-raw", "pathwaysXLSX.R", package = "FEDUP")

+#' system.file("data-raw", "pathwaysXLSX.R", package="FEDUP")

 #'

 #' @format a named list of 30 vectors

 "pathwaysXLSX"

@@ -27,10 +27,10 @@

 #' Example list of yeast SAFE terms obtained from a TXT file.

 #'

 #' Raw data location

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

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

 #'

 #' Script to prepare data

-#' system.file("data-raw", "pathwaysTXT.R", package = "FEDUP")

+#' system.file("data-raw", "pathwaysTXT.R", package="FEDUP")

 #'

 #' @format a named list of 30 vectors

 "pathwaysTXT"

@@ -38,7 +38,7 @@

 #' Example vector of human genes to use as test set for enrichment.

 #'

 #' Script to prepare data

-#' system.file("data-raw", "genes.R", package = "FEDUP")

+#' system.file("data-raw", "genes.R", package="FEDUP")

 #'

 #' @format a character vector with 190 elements (gene IDs)

 "testGene"

@@ -46,7 +46,7 @@

 #' Example vector of human genes to use as background set for enrichment.

 #'

 #' Script to generate data

-#' system.file("data-raw", "genes.R", package = "FEDUP")

+#' system.file("data-raw", "genes.R", package="FEDUP")

 #'

 #' @format a character vector with 10208 elements (gene IDs)

 "backgroundGene"

@@ -1,37 +1,42 @@

-inputObject <- function(test_gene, background_gene, pathways) {

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

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

-    test_gene_in_pathways <- which(test_gene %in% pathway_genes)

-    back_gene_in_pathways <- which(background_gene %in% pathway_genes)

+    testGene_in_pathways <- which(testGene %in% pathway_genes)

+    back_gene_in_pathways <- which(backgroundGene %in% pathway_genes)

-    if (is.null(test_gene)) {

-        stop("Oops, argument 'test_gene' is empty. Supply a vector of

-         genes ... I promise this will work.")

-    } else if (is.null(background_gene)) {

-        stop("Oops, argument 'background_gene' is empty. Supply a vector of

-        genes ... I promise this will work")

-    } else if (!is.list(pathways)) {

+    if (is.null(testGene)) {

+        stop("Oops, argument 'testGene' is empty. Supply a vector of

+        genes... I promise this will work.")

+    }

+    if (is.null(backgroundGene)) {

+        stop("Oops, argument 'backgroundGene' is empty. Supply a vector of

+        genes... I promise this will work.")

+    }

+    if (!is.list(pathways)) {

         stop("Oops, argument 'pathways' is not in a list format...

         have you tried using readPathways() on your input pathway file?")

-    } else if (!length(test_gene_in_pathways)) {

-        stop("Oops, none of the genes in 'test_gene' was found in 'pathways'.

+    }

+    if (!length(testGene_in_pathways)) {

+        stop("Oops, none of the genes in 'testGene' was found in 'pathways'.

         Make sure that you have some gene IDs in both inputs, otherwise how do

         you expect this works?")

-    } else if (!length(back_gene_in_pathways)) {

-        stop("Oops, none of the genes in 'background_genes' was found in

+    }

+    if (!length(back_gene_in_pathways)) {

+        stop("Oops, none of the genes in 'backgroundGenes' was found in

         'pathways'. Make sure that you have some gene IDs in both inputs,

         otherwise how do you expect this works?")

-    } else if (length(test_gene) >= length(background_gene)) {

+    }

+    if (length(testGene) >= length(backgroundGene)) {

         stop("Oops, your test set can't have more genes than your background

-        set. Have you mixed up the 'test_gene' and 'background_gene' arguments?

+        set. Have you mixed up the 'testGene' and 'backgroundGene' arguments?

         You're so close... I can feel it.")

     }

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

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

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

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

-    list(test_gene = test_gene,

-        background_gene = background_gene,

+    list(testGene = testGene,

+        backgroundGene = backgroundGene,

         pathways = pathways,

         pathways_name = names(pathways),

         pathways_size = unlist(lapply(pathways, length))

@@ -40,8 +45,8 @@ inputObject <- function(test_gene, background_gene, pathways) {

 #' Runs gene enrichment and depletion analysis for a list of pathways.

 #'

-#' @param test_gene (char) vector of genes to use as test set.

-#' @param background_gene (char) vector of genes to use as background set.

+#' @param testGene (char) vector of genes to use as test set.

+#' @param backgroundGene (char) vector of genes to use as background set.

 #' @param pathways (list) list of vectors with pathway annotations.

 #' @return table of pathway enrichment and depletion results. Rows represent

 #' tested pathways. Columns represent:

@@ -49,14 +54,14 @@ inputObject <- function(test_gene, background_gene, pathways) {

 #'     \item pathway -- name of the pathway, corresponds to

 #'         names(\code{pathways});

 #'     \item size -- size of the pathway;

-#'     \item real_frac -- fraction of \code{test_gene} members in pathway;

-#'     \item expected_frac -- fraction of \code{background_gene} members in

+#'     \item real_frac -- fraction of \code{testGene} members in pathway;

+#'     \item expected_frac -- fraction of \code{backgroundGene} members in

 #'         pathway;

 #'     \item fold_enrichment -- fold enrichment measure,

 #'         evaluates as \code{real_frac} / \code{expected_frac};

 #'     \item status -- indicator that pathway is enriched or depleted for

-#'         \code{test_gene} members;

-#'     \item real_gene -- vector of \code{test_gene} gene members annotated

+#'         \code{testGene} members;

+#'     \item real_gene -- vector of \code{testGene} gene members annotated

 #'         to \code{pathways};

 #'     \item pvalue -- enrichment p-value calculated via Fisher's exact test;

 #'     \item qvalue -- BH-adjusted p-value

@@ -70,10 +75,10 @@ inputObject <- function(test_gene, background_gene, pathways) {

 #' @importFrom utils head read.delim tail

 #' @importFrom stats fisher.test p.adjust

 #' @export

-runFedup <- function(test_gene, background_gene, pathways) {

-    inputs <- inputObject(test_gene, background_gene, pathways)

-    test <- inputs$test_gene

-    background <- inputs$background_gene

+runFedup <- function(testGene, backgroundGene, pathways) {

+    inputs <- inputObject(testGene, backgroundGene, pathways)

+    test <- inputs$testGene

+    background <- inputs$backgroundGene

     pathways <- inputs$pathways

     pathways_name <- inputs$pathways_name

     pathways_size <- inputs$pathways_size

@@ -84,17 +89,17 @@ runFedup <- function(test_gene, background_gene, pathways) {

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

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

-        a_n <- length(test) # n test genes

-        b_n <- length(background) # n background genes

-        a <- intersect(test, x) # test genes in pathway

-        b <- intersect(background, x) # background genes in pathway

-        a_len <- length(a) # n test genes in pathway

-        b_len <- length(b) # n background genes in pathway

-        a_x <- (a_len / a_n) * 100 # fraction of test genes in pathway

-        b_x <- (b_len / b_n) * 100 # fraction of background genes in pathway

-        f <- a_x / b_x # fold enrichment measure

+        a_n <- length(test)

+        b_n <- length(background)

+        a <- intersect(test, x)

+        b <- intersect(background, x)

+        a_len <- length(a)

+        b_len <- length(b)

+        a_x <- (a_len / a_n) * 100

+        b_x <- (b_len / b_n) * 100

+        f <- a_x / b_x

         e <- ifelse(f > 1, "Enriched", "Depleted")

-        m <- rbind(c(a_len, b_len), c(a_n, b_n)) # pval contingency table

+        m <- rbind(c(a_len, b_len), c(a_n, b_n))

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

         return(c(

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

@@ -107,8 +112,9 @@ runFedup <- function(test_gene, background_gene, pathways) {

     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),] # BH-correct pvalues

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

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

+

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

     return(res)

 }

@@ -2,7 +2,7 @@

 #'

 #' @param df (data.frame) table with FEDUP enrichment results.

 #'  (see runFedup() for column descriptions)

-#' @param results_file (char) name of output results file.

+#' @param resultsFile (char) name of output results file.

 #' @return table of gene enrichment and depletion results formatted as a

 #' 'Generic results file'. Rows represent tested pathways. Columns represent:

 #' \itemize{

@@ -11,43 +11,42 @@

 #'     \item description -- pathway name or description;

 #'     \item pvalue -- enrichment pvalue;

 #'     \item qvalue -- BH-corrected pvalue;

-#'     \item status -- +1 or -1, to identify enrichment in either of the two

-#'         phenotypes being compared in the two-class analysis

+#'     \item status -- +1 or -1, to identify enriched or depleted pathways

 #'         (+1 maps to red, -1 maps to blue)

 #' }

 #' @examples

 #' data(testGene)

 #' data(backgroundGene)

 #' data(pathwaysGMT)

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

-#' results_file <- tempfile("fedup_res", fileext = ".txt")

-#' writeFemap(fedup_res, results_file)

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

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

+#' writeFemap(fedupRes, resultsFile)

 #' @importFrom data.table fwrite

 #' @importFrom dplyr select mutate %>%

 #' @export

-writeFemap <- function(df, results_file) {

+writeFemap <- function(df, resultsFile) {

     df_em <- df %>%

         select("pathway", "pvalue", "qvalue", "status") %>%

         mutate("description" = gsub("\\%.*", "", df$pathway)) %>%

         mutate("status" = ifelse(df$status == "Enriched", "1", "-1")) %>%

         select("pathway", "description", "pvalue", "qvalue", "status")

-    fwrite(df_em, results_file, sep = "\t", col.names = TRUE, quote = FALSE)

-    message("Wrote Cytoscape-formatted FEDUP results file to ", results_file)

+    fwrite(df_em, resultsFile, sep = "\t", col.names = TRUE, quote = FALSE)

+    message("Wrote out Cytoscape-formatted FEDUP results file to ", resultsFile)

 }

 #' Draws a network representation of overlaps among enriched and depleted

 #' pathways using EnrichmentMap (EM) in Cytoscape.

 #'

-#' @param gmt_file (char) path to GMT file (must be an absolute path).

-#' @param results_file (char) path to file with FEDUP results

+#' @param gmtFile (char) path to GMT file (must be an absolute path).

+#' @param resultsFile (char) path to file with FEDUP results

 #'  (must be an absolute path).

 #' @param pvalue (numeric) pvalue cutoff. Pathways with a higher pvalue

 #'  will not be included in the EM (value between 0 and 1; default 1).

 #' @param qvalue (numeric) qvalue cutoff. Pathways with a higher qvalue

 #'  will not be included in the EM (value between 0 and 1; default 1).

-#' @param net_name (char) name for EM in Cytoscape (default generic).

-#' @param net_file (char) name of output image. Supports png, pdf, svg,

+#' @param netName (char) name for EM in Cytoscape (default generic).

+#' @param netFile (char) name of output image. Supports png, pdf, svg,

 #'  jpeg image formats.

 #' @return file name of image to which the network is exported. Also side

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

@@ -57,41 +56,39 @@ writeFemap <- function(df, results_file) {

 #'     data(testGene)

 #'     data(backgroundGene)

 #'     data(pathwaysGMT)

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

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

-#'     results_file <- tempfile("fedup_res", fileext = ".txt")

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

-#'     writePathways(pathwaysGMT, gmt_file)

-#'     writeFemap(fedup_res, results_file)

+#'     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(

-#'         gmt_file = gmt_file,

-#'         results_file = results_file,

-#'         qvalue = 0.05,

-#'         net_name = "FEDUP_EM",

-#'         net_file = net_file)}

+#'         gmtFile=gmtFile,

+#'         resultsFile=resultsFile,

+#'         qvalue=0.05,

+#'         netName="FEDUP_EM",

+#'         netFile=netFile)}

 #' @import RCy3

 #' @export

-plotFemap <- function(gmt_file, results_file,

-                        pvalue = 1, qvalue = 1,

-                        net_name = "generic", net_file = "png") {

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

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

+

     # Confirm that Cytoscape is installed and opened

     cytoscapePing()

-    if (net_name %in% getNetworkList()) {

-        deleteNetwork(net_name)

-    }

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

     message("Building the network")

     em_command <- paste(

         'enrichmentmap build analysisType="generic"',

-        "gmtFile=", gmt_file,

-        "enrichmentsDataset1=", results_file,

+        "gmtFile=", gmtFile,

+        "enrichmentsDataset1=", resultsFile,

         "pvalue=", pvalue,

         "qvalue=", qvalue,

         "similaritycutoff=", 0.375,

         "coefficients=", "COMBINED",

         "combinedConstant=", 0.5)

     response <- commandsGET(em_command)

-    renameNetwork(net_name, getNetworkSuid())

+    renameNetwork(netName, getNetworkSuid())

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

     message("Setting network chart data")

@@ -106,18 +103,18 @@ plotFemap <- function(gmt_file, results_file,

         "autoannotate annotate-clusterBoosted",

         "clusterAlgorithm=MCL",

         "maxWords=3",

-        "network=", net_name)

+        "network=", netName)

     response <- commandsGET(aa_command)

     # Network layout

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

     ln_command <- paste(

         "layout force-directed",

-        "network=", net_name)

+        "network=", netName)

     response <- commandsGET(ln_command)

     fitContent()

     # Draw out network to file

-    message("Drawing out network to ", net_file)

-    exportImage(net_file)

+    message("Drawing out network to ", netFile)

+    exportImage(netFile)

 }

@@ -1,83 +1,83 @@

 #' Returns a list of pathways from various file formats.

-#' Currently supports the following file format: GMT, TXT, XLSX.

+#' Currently supports the following file format: gmt, txt, xlsx.

 #'

-#' @param pathway_file (char) path to file with pathway annotations.

-#' @param header (logical) whether \code{pathway_file} has a header

+#' @param pathwayFile (char) path to file with pathway annotations.

+#' @param header (logical) whether \code{pathwayFile} has a header

 #'     (default FALSE).

-#' @param pathway_col (char) column name with pathway identifiers.

+#' @param pathwayCol (char) column name with pathway identifiers.

 #'     For use with non-GMT input files (eg "Pathway.ID"; default NULL).

-#' @param gene_col (char) column name with gene identifiers.

+#' @param geneCol (char) column name with gene identifiers.

 #'     For use with non-GMT input files (eg "Gene.ID"; default NULL).

-#' @param MIN_GENE (integer) minimum number of genes to be considered

-#'     in a pathway (default = 1).

-#' @param MAX_GENE (integer) maximum number of genes to be considered

-#'     in a pathway (default = Inf).

+#' @param minGene (integer) minimum number of genes to be considered

+#'     in a pathway (default 1).

+#' @param maxGene (integer) maximum number of genes to be considered

+#'     in a pathway (default Inf).

 #' @return a list of vectors with pathway annotations.

 #' @examples

 #' pathways <- readPathways(

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

-#'     package = "FEDUP"), MIN_GENE = 10, MAX_GENE = 500)

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

 #' pathways <- readPathways(

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

-#'     header = TRUE, pathway_col = "Enriched.GO.names", gene_col = "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(pathway_file, header = FALSE,

-                        pathway_col = NULL, gene_col = NULL,

-                        MIN_GENE = 1L, MAX_GENE = Inf) {

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

+                        pathwayCol=NULL, geneCol=NULL,

+                        minGene=1L, maxGene=Inf) {

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

-    s <- c("gmt", "txt", "xlsx") # supported file extensions

-    f <- sub(".*\\.", "", pathway_file) # pathway_file extension

+    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 = ", "), "."))

     }

     if (f == "gmt") {

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

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

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

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

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

     } else {

         if (f == "xlsx") {

-            pathway_in <- read.xlsx(pathway_file)

+            pathway_in <- read.xlsx(pathwayFile)

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

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

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

         }

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

-            stop("Pathway ID column (", pathway_col, ") not in file")

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

-            stop("Gene ID column (", gene_col, ") not in file")

+        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)) {

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

         } else {

             pathway_df <- data.frame(

-                pathway = pathway_in[,pathway_col],

-                gene = pathway_in[,gene_col])

+                pathway = pathway_in[,pathwayCol],

+                gene = pathway_in[,geneCol])

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

-            pathway_df <- na.omit(pathway_df) # ensure no NaNs

+            pathway_df <- na.omit(pathway_df)

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

-            pathways <- deframe(pathway_df) # transform df to list

+            pathways <- deframe(pathway_df)

         }

     }

-    size <- lapply(pathways, length) # subset for pathways in [MIN:MAX] range

-    pathways_s <- pathways[which(size >= MIN_GENE & size <= MAX_GENE)]

+    size <- lapply(pathways, length)

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

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

-    message(" => n total pathways: ", length(pathways))

-    message(" => n pathways (",MIN_GENE,"-",MAX_GENE, "): ", length(pathways_s))

-

     if (!length(pathways_s)) {

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

     }

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

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

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

+

     return(pathways_s)

 }

 #' Writes a set of pathways (list of vectors) to a GMT file.

 #'

 #' @param pathways (list) named list of vectors.

-#' @param gmt_file (char) name of output GMT file.

+#' @param gmtFile (char) name of output GMT file.

 #' @return GMT-formatted file. Rows represent pathways. Columns represent:

 #' \itemize{

 #'     \item pathway ID;

@@ -86,15 +86,15 @@ readPathways <- function(pathway_file, 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, gmt_file) {

+writePathways <- function(pathways, gmtFile) {

     tab <- data.table(

         pathway = names(pathways),

         description = gsub("\\%.*", "", names(pathways)),

         genes = unlist(lapply(pathways, paste, collapse = "\t"))

     )

-    fwrite(tab, file = gmt_file, sep = "\t", col.names = FALSE, quote = FALSE)

-    message("Wrote out GMT file with to ", gmt_file)

+    fwrite(tab, file = gmtFile, sep = "\t", col.names = FALSE, quote = FALSE)

+    message("Wrote out pathway gmt file to ", gmtFile)

 }

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

 #' Visualizes pathway enrichment and depletion using ggplot.

 #'

 #' @param df (data.frame) table with FEDUP enrichment results to plot.

-#' @param x_var (char) x-axis variable (must be a column value in \code{df}).

-#' @param y_var (char) y-axis variable (must be a column value in \code{df}).

-#' @param x_lab (char) x-axis label (default \code{x_var} value).

-#' @param y_lab (char) y-axis label (default NULL).

-#' @param p_title (char) plot title (default NULL).

-#' @param fill_var (char) point fill variable (default NULL).

-#' @param fill_col (char) point fill colours (default NULL).

-#' @param fill_lab (char) point fill label (default \code{fill_var} value).

-#' @param size_var (char) point size variable (default NULL).

-#' @param size_lab (char) point size label (default \code{size_var} value).

+#' @param xVar (char) x-axis variable (must be a column value in \code{df}).

+#' @param yVar (char) y-axis variable (must be a column value in \code{df}).

+#' @param xLab (char) x-axis label (default \code{xVar} value).

+#' @param yLab (char) y-axis label (default NULL).

+#' @param pTitle (char) plot title (default NULL).

+#' @param fillVar (char) point fill variable (default NULL).

+#' @param fillCol (char) point fill colours (default NULL).

+#' @param fillLab (char) point fill label (default \code{fillVar} value).

+#' @param sizeVar (char) point size variable (default NULL).

+#' @param sizeLab (char) point size label (default \code{sizeVar} value).

 #' @return object returned from ggplot with the enrichment dot plot.

 #' @examples

 #' data(testGene)

@@ -21,55 +21,56 @@

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

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

 #' plotDotPlot(

-#'     df = fedup_plot,

-#'     x_var = "log10qvalue",

-#'     y_var = "pathway",

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

-#'     fill_var = "status",

-#'     fill_lab = "Enrichment\nstatus",

-#'     size_var = "fold_enrichment",

-#'     size_lab = "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, x_var, y_var,

-                        x_lab = x_var, y_lab = NULL, p_title = NULL,

-                        fill_var = NULL, fill_col = NULL, fill_lab = fill_var,

-                        size_var = NULL, size_lab = size_var) {

+plotDotPlot <- function(df, xVar, yVar,

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

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

+                        sizeVar=NULL, sizeLab=sizeVar) {

-    if (!is.null(fill_var) && is.null(fill_col)) {

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

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

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

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

-        fill_col <- brewer.pal(pal_n, "Set1")

+        fillCol <- brewer.pal(pal_n, "Set1")

     }

-    if (fill_var == "status") {

-        df[[fill_var]] <- factor(

-            df[[fill_var]],

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

+    if (fillVar == "status") {

+        df[[fillVar]] <- factor(

+            df[[fillVar]],

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

     }

     p <- ggplot(df, aes_string(

-                x = x_var,

-                y = fct_reorder(df[[y_var]], df[[x_var]]),

-                fill = fill_var,

-                size = size_var)) +

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

-        labs(x = x_lab, y = y_lab, title = p_title,

-            fill = fill_lab, size = size_lab) +

-        scale_fill_manual(values = fill_col) +

-        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())

-    if (is.numeric(df[[x_var]])) {

-        xmin <- floor(min(df[[x_var]])) # set x-axis limits to avoid points

-        xmax <- ceiling(max(df[[x_var]])) # being cut off from plot window

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

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

+        xmin <- floor(min(df[[xVar]]))

+        xmax <- ceiling(max(df[[xVar]]))

         p <- p + xlim(xmin, xmax)

     }

     return(p)

@@ -12,6 +12,6 @@ backgroundGene

 }

 \description{

 Script to generate data

-system.file("data-raw", "genes.R", package = "FEDUP")

+system.file("data-raw", "genes.R", package="FEDUP")

 }

 \keyword{datasets}

@@ -18,8 +18,8 @@ Raw GMT file is available from

 \details{

 Raw data location

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

-    package = "FEDUP")

+    package="FEDUP")

 Script to prepare data

-system.file("data-raw", "pathwaysGMT.R", package = "FEDUP")

+system.file("data-raw", "pathwaysGMT.R", package="FEDUP")

 }

 \keyword{datasets}

@@ -12,10 +12,10 @@ pathwaysTXT

 }

 \description{

 Raw data location

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

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

 }

 \details{

 Script to prepare data

-system.file("data-raw", "pathwaysTXT.R", package = "FEDUP")

+system.file("data-raw", "pathwaysTXT.R", package="FEDUP")

 }

 \keyword{datasets}

@@ -12,10 +12,10 @@ pathwaysXLSX

 }

 \description{

 Raw data location

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

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

 }

 \details{

 Script to prepare data

-system.file("data-raw", "pathwaysXLSX.R", package = "FEDUP")

+system.file("data-raw", "pathwaysXLSX.R", package="FEDUP")

 }

 \keyword{datasets}

@@ -6,40 +6,40 @@

 \usage{

 plotDotPlot(

   df,

-  x_var,

-  y_var,

-  x_lab = x_var,

-  y_lab = NULL,

-  p_title = NULL,

-  fill_var = NULL,

-  fill_col = NULL,

-  fill_lab = fill_var,

-  size_var = NULL,

-  size_lab = size_var

+  xVar,

+  yVar,

+  xLab = xVar,

+  yLab = NULL,

+  pTitle = NULL,

+  fillVar = NULL,

+  fillCol = NULL,

+  fillLab = fillVar,

+  sizeVar = NULL,

+  sizeLab = sizeVar

 )

 }

 \arguments{

 \item{df}{(data.frame) table with FEDUP enrichment results to plot.}

-\item{x_var}{(char) x-axis variable (must be a column value in \code{df}).}

+\item{xVar}{(char) x-axis variable (must be a column value in \code{df}).}

-\item{y_var}{(char) y-axis variable (must be a column value in \code{df}).}

+\item{yVar}{(char) y-axis variable (must be a column value in \code{df}).}

-\item{x_lab}{(char) x-axis label (default \code{x_var} value).}

+\item{xLab}{(char) x-axis label (default \code{xVar} value).}

-\item{y_lab}{(char) y-axis label (default NULL).}

+\item{yLab}{(char) y-axis label (default NULL).}

-\item{p_title}{(char) plot title (default NULL).}

+\item{pTitle}{(char) plot title (default NULL).}

-\item{fill_var}{(char) point fill variable (default NULL).}

+\item{fillVar}{(char) point fill variable (default NULL).}

-\item{fill_col}{(char) point fill colours (default NULL).}

+\item{fillCol}{(char) point fill colours (default NULL).}

-\item{fill_lab}{(char) point fill label (default \code{fill_var} value).}

+\item{fillLab}{(char) point fill label (default \code{fillVar} value).}

-\item{size_var}{(char) point size variable (default NULL).}

+\item{sizeVar}{(char) point size variable (default NULL).}

-\item{size_lab}{(char) point size label (default \code{size_var} value).}

+\item{sizeLab}{(char) point size label (default \code{sizeVar} value).}

 }

 \value{

 object returned from ggplot with the enrichment dot plot.

@@ -56,12 +56,12 @@ 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,

-    x_var = "log10qvalue",

-    y_var = "pathway",

-    x_lab = "-log10(Qvalue)",

-    fill_var = "status",

-    fill_lab = "Enrichment\nstatus",

-    size_var = "fold_enrichment",

-    size_lab = "Fold enrichment")

+    df=fedup_plot,

+    xVar="log10qvalue",

+    yVar="pathway",

+    xLab="-log10(Qvalue)",

+    fillVar="status",

+    fillLab="Enrichment\nstatus",

+    sizeVar="fold_enrichment",

+    sizeLab="Fold enrichment")

 }

@@ -6,18 +6,18 @@

 pathways using EnrichmentMap (EM) in Cytoscape.}

 \usage{

 plotFemap(

-  gmt_file,

-  results_file,

+  gmtFile,

+  resultsFile,

   pvalue = 1,

   qvalue = 1,

-  net_name = "generic",

-  net_file = "png"

+  netName = "generic",

+  netFile = "png"

 )

 }

 \arguments{

-\item{gmt_file}{(char) path to GMT file (must be an absolute path).}

+\item{gmtFile}{(char) path to GMT file (must be an absolute path).}

-\item{results_file}{(char) path to file with FEDUP results

+\item{resultsFile}{(char) path to file with FEDUP results

 (must be an absolute path).}

 \item{pvalue}{(numeric) pvalue cutoff. Pathways with a higher pvalue

@@ -26,9 +26,9 @@ will not be included in the EM (value between 0 and 1; default 1).}

 \item{qvalue}{(numeric) qvalue cutoff. Pathways with a higher qvalue

 will not be included in the EM (value between 0 and 1; default 1).}

-\item{net_name}{(char) name for EM in Cytoscape (default generic).}

+\item{netName}{(char) name for EM in Cytoscape (default generic).}

-\item{net_file}{(char) name of output image. Supports png, pdf, svg,

+\item{netFile}{(char) name of output image. Supports png, pdf, svg,

 jpeg image formats.}

 }

 \value{

@@ -45,16 +45,16 @@ pathways using EnrichmentMap (EM) in Cytoscape.

     data(testGene)

     data(backgroundGene)

     data(pathwaysGMT)

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

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

-    results_file <- tempfile("fedup_res", fileext = ".txt")

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

-    writePathways(pathwaysGMT, gmt_file)

-    writeFemap(fedup_res, results_file)

+    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(

-        gmt_file = gmt_file,

-        results_file = results_file,

-        qvalue = 0.05,

-        net_name = "FEDUP_EM",

-        net_file = net_file)}

+        gmtFile=gmtFile,

+        resultsFile=resultsFile,

+        qvalue=0.05,

+        netName="FEDUP_EM",

+        netFile=netFile)}

 }

@@ -3,47 +3,47 @@

 \name{readPathways}

 \alias{readPathways}

 \title{Returns a list of pathways from various file formats.

-Currently supports the following file format: GMT, TXT, XLSX.}

+Currently supports the following file format: gmt, txt, xlsx.}

 \usage{

 readPathways(

-  pathway_file,

+  pathwayFile,

   header = FALSE,

-  pathway_col = NULL,

-  gene_col = NULL,

-  MIN_GENE = 1L,

-  MAX_GENE = Inf

+  pathwayCol = NULL,

+  geneCol = NULL,

+  minGene = 1L,

+  maxGene = Inf

 )

 }

 \arguments{

-\item{pathway_file}{(char) path to file with pathway annotations.}

+\item{pathwayFile}{(char) path to file with pathway annotations.}

-\item{header}{(logical) whether \code{pathway_file} has a header

+\item{header}{(logical) whether \code{pathwayFile} has a header

 (default FALSE).}

-\item{pathway_col}{(char) column name with pathway identifiers.

+\item{pathwayCol}{(char) column name with pathway identifiers.

 For use with non-GMT input files (eg "Pathway.ID"; default NULL).}

-\item{gene_col}{(char) column name with gene identifiers.

+\item{geneCol}{(char) column name with gene identifiers.

 For use with non-GMT input files (eg "Gene.ID"; default NULL).}

-\item{MIN_GENE}{(integer) minimum number of genes to be considered

-in a pathway (default = 1).}

+\item{minGene}{(integer) minimum number of genes to be considered

+in a pathway (default 1).}

-\item{MAX_GENE}{(integer) maximum number of genes to be considered

-in a pathway (default = Inf).}

+\item{maxGene}{(integer) maximum number of genes to be considered

+in a pathway (default Inf).}

 }

 \value{

 a list of vectors with pathway annotations.

 }

 \description{

 Returns a list of pathways from various file formats.

-Currently supports the following file format: GMT, TXT, XLSX.

+Currently supports the following file format: gmt, txt, xlsx.

 }

 \examples{

 pathways <- readPathways(

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

-    package = "FEDUP"), MIN_GENE = 10, MAX_GENE = 500)

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

 pathways <- readPathways(

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

-    header = TRUE, pathway_col = "Enriched.GO.names", gene_col = "Gene.ID")

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

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

 }

@@ -4,12 +4,12 @@

 \alias{runFedup}

 \title{Runs gene enrichment and depletion analysis for a list of pathways.}

 \usage{

-runFedup(test_gene, background_gene, pathways)