Add examples

R/doPCA.R

@@ -47,6 +47,14 @@
 #'  components.}
 #' }
 #'
+#' @examples
+#' sce <- readRDS(system.file("extdata", "mq_example", "1356_sce.rds",
+#'                            package = "einprot"))
+#' pca <- doPCA(sce, assayName = "log2_LFQ.intensity", ncomponents = 3)
+#' pca$plotcoord$PC1_2
+#' pca$plotcombined$PC1_2
+#' pca$plotpairs
+#'
 #' @importFrom scater runPCA
 #' @importFrom scuttle makePerCellDF
 #' @importFrom tibble rownames_to_column

R/makeAbundanceExport.R

@@ -13,6 +13,14 @@
 #'
 #' @returns A \code{data.frame} with abundances for significant features.
 #'
+#' @examples
+#' sce <- readRDS(system.file("extdata", "mq_example", "1356_sce.rds",
+#'                            package = "einprot"))
+#' names(S4Vectors::metadata(sce)$testres$tests)
+#' abExp <- makeAbundanceExport(S4Vectors::metadata(sce)$testres$tests,
+#'                              abundancePrefix = "iBAQ")
+#' head(abExp)
+#'
 #' @importFrom dplyr select filter starts_with contains if_any full_join
 #'     matches everything
 #'

R/makeAbundanceHeatmap.R

@@ -28,6 +28,13 @@
 #'
 #' @returns A ComplexHeatmap object.
 #'
+#' @examples
+#' sce <- readRDS(system.file("extdata", "mq_example", "1356_sce.rds",
+#'                            package = "einprot"))
+#' hm <- makeAbundanceHeatmap(sce, assayToPlot = "log2_LFQ.intensity",
+#'                            doCenter = TRUE, settings = "report")
+#' ComplexHeatmap::draw(hm)
+#'
 #' @importFrom ComplexHeatmap Heatmap columnAnnotation
 #' @importFrom SummarizedExperiment assay assayNames
 #' @importFrom grid gpar

R/makeiSEEScript.R

@@ -18,6 +18,19 @@
 #'
 #' @returns The path to the generated script.
 #'
+#' @examples
+#' sceFile <- system.file("extdata", "mq_example", "1356_sce.rds",
+#'                        package = "einprot")
+#' sce <- readRDS(sceFile)
+#' isee <- makeiSEEScript(tempfile(fileext = "_isee.R"), sceFile = sceFile,
+#'                        aName = "LFQ.intensity",
+#'                        tests = S4Vectors::metadata(sce)$testres$tests,
+#'                        assayForPlots = "log2_LFQ.intensity",
+#'                        assayForHeatmaps = "iBAQ",
+#'                        includeFeatureSetTable = FALSE)
+#' file.exists(isee)
+#' head(readLines(isee), 10)
+#'
 #' @author Charlotte Soneson
 #' @export
 #'

R/plotImputation.R

@@ -15,6 +15,12 @@
 #'
 #' @returns A ggplot object.
 #'
+#' @examples
+#' sce <- readRDS(system.file("extdata", "mq_example", "1356_sce.rds",
+#'                            package = "einprot"))
+#' plotImputationDistribution(sce, assayToPlot = "log2_LFQ.intensity",
+#'                            assayImputation = "imputed_LFQ.intensity")
+#'
 #' @importFrom SummarizedExperiment assay
 #' @importFrom tibble rownames_to_column
 #' @importFrom tidyr gather

R/plotMissingValues.R

@@ -59,6 +59,11 @@ plotMissingValuesHeatmap <- function(sce, assayMissing) {
 #'
 #' @returns A \code{ggplot} object.
 #'
+#' @examples
+#' sce <- readRDS(system.file("extdata", "mq_example", "1356_sce.rds",
+#'                            package = "einprot"))
+#' plotFractionDetectedPerSample(SummarizedExperiment::colData(sce))
+#'
 #' @importFrom ggplot2 ggplot aes theme geom_bar theme_bw labs expand_limits
 #'     geom_text
 #' @importFrom dplyr filter %>%
@@ -96,6 +101,11 @@ plotFractionDetectedPerSample <- function(dfNA) {
 #'
 #' @returns A \code{ggplot} object.
 #'
+#' @examples
+#' sce <- readRDS(system.file("extdata", "mq_example", "1356_sce.rds",
+#'                            package = "einprot"))
+#' plotDetectedInSamples(SummarizedExperiment::rowData(sce))
+#'
 #' @importFrom ggplot2 ggplot aes geom_bar labs
 #' @importFrom rlang .data
 #' @importFrom dplyr filter %>% group_by tally pull mutate

R/plotVolcano.R

@@ -330,6 +330,18 @@
 #'     If \code{baseFileName} is not \code{NULL}, pdf files with volcano
 #'     plots and bar plots for significant complexes will also be generated.
 #'
+#' @examples
+#' sce <- readRDS(system.file("extdata", "mq_example", "1356_sce.rds",
+#'                            package = "einprot"))
+#' tres <- runTest(sce, comparisons = list(c("RBC_ctrl", "Adnp")),
+#'                 testType = "limma", assayForTests = "log2_LFQ.intensity",
+#'                 assayImputation = "imputed_LFQ.intensity")
+#' pv <- plotVolcano(sce, tres$tests$Adnp_vs_RBC_ctrl, testType = "limma",
+#'                   comparisonString = "Adnp_vs_RBC_ctrl")
+#' pv$gg
+#' pv$ggma
+#' pv$ggwf
+#'
 #' @author Charlotte Soneson
 #' @export
 #' @importFrom ggplot2 geom_point aes labs

R/prepareFeatureCollections.R

@@ -60,6 +60,21 @@
 #'
 #' @returns A list of \code{CharacterList}s (one for each feature collection).
 #'
+#' @examples
+#' sce <- readRDS(system.file("extdata", "mq_example", "1356_sce.rds",
+#'                            package = "einprot"))
+#' fc <- prepareFeatureCollections(sce, idCol = "einprotGene",
+#'                                 includeFeatureCollections = "complexes",
+#'                                 complexDbPath = NULL,
+#'                                 speciesInfo = getSpeciesInfo("mouse"),
+#'                                 complexSpecies = "all")
+#'
+#' ## List of complexes, expressed in terms of the row names of sce
+#' fc
+#'
+#' ## Metadata for the complexes
+#' S4Vectors::mcols(fc$complexes)
+#'
 #' @importFrom S4Vectors mcols DataFrame endoapply
 #' @importFrom IRanges CharacterList
 #' @importFrom methods as
@@ -82,6 +97,10 @@ prepareFeatureCollections <- function(sce, idCol, includeFeatureCollections,
     .assertVector(x = includeFeatureCollections, type = "character",
                   validValues = c("complexes", "GO"), allowNULL = TRUE)
     .assertScalar(x = complexDbPath, type = "character", allowNULL = TRUE)
+    if (is.null(complexDbPath) && "complexes" %in% includeFeatureCollections) {
+        complexDbPath <- system.file(EINPROT_COMPLEXES_FILE,
+                                     package = "einprot")
+    }
     if (!is.null(complexDbPath)) {
         stopifnot(file.exists(complexDbPath))
     }

R/runTests.R

@@ -287,6 +287,15 @@
 #' (including only features and feature sets passing the imposed significance
 #' thresholds) are saved.
 #'
+#' @examples
+#' sce <- readRDS(system.file("extdata", "mq_example", "1356_sce.rds",
+#'                            package = "einprot"))
+#' tres <- runTest(sce, comparisons = list(c("RBC_ctrl", "Adnp")),
+#'                 testType = "limma", assayForTests = "log2_LFQ.intensity",
+#'                 assayImputation = "imputed_LFQ.intensity")
+#' head(tres$tests$Adnp_vs_RBC_ctrl)
+#' tres$design
+#'
 #' @importFrom SummarizedExperiment assay rowData colData
 #' @importFrom stats model.matrix p.adjust
 #' @importFrom limma lmFit treat topTreat cameraPR ids2indices eBayes

R/summaryPlots.R

@@ -138,6 +138,15 @@ makeMeanSDPlot <- function(sce, assayName, xlab = "Mean", ylab = "SD") {
 #'
 #' @returns A \code{cowplot} object
 #'
+#' @examples
+#' sce <- readRDS(system.file("extdata", "mq_example", "1356_sce.rds",
+#'                            package = "einprot"))
+#' tres <- runTest(sce, comparisons = list(c("RBC_ctrl", "Adnp"),
+#'                                         c("RBC_ctrl", "Chd4BF")),
+#'                 testType = "limma", assayForTests = "log2_LFQ.intensity",
+#'                 assayImputation = "imputed_LFQ.intensity")
+#' makeSAPlot(tres$tests)
+#'
 #' @export
 #' @author Charlotte Soneson
 #'

inst/scripts/generate_mq_sce.R

@@ -0,0 +1,19 @@
+library(einprot)
+sampleAnnot <- read.delim(system.file("extdata", "mq_example",
+                                      "1356_sampleAnnot.txt",
+                                      package = "einprot"))
+out <- runMaxQuantAnalysis(
+    outputDir = "~/Desktop/1356_mq",
+    outputBaseName = "1356",
+    forceOverwrite = TRUE,
+    species = "mouse",
+    mqFile = system.file("extdata", "mq_example", "1356_proteinGroups.txt",
+                         package = "einprot"),
+    mqParameterFile = system.file("extdata", "mq_example", "1356_mqpar.xml",
+                                  package = "einprot"),
+    iColPattern = "^LFQ.intensity.",
+    sampleAnnot = sampleAnnot,
+    ctrlGroup = "RBC_ctrl",
+    stringIdCol = NULL,
+    includeFeatureCollections = "complexes"
+)