Tag: RDocumentation

labkey.experiment.saveRuns function – RDocumentation

Examples # NOT RUN { library(Rlabkey) ## example with materialInputs and materialOutputs m1 <- labkey.experiment.createMaterial( list(name = “87444063.2604.626”), sampleSetName = “Study Specimens”) m2 <- labkey.experiment.createMaterial( list(name = “87444063.2604.625”), sampleSetName = “Study Specimens”) run <- labkey.experiment.createRun( list(name=”new run”), materialInputs = m1, materialOutputs = m2) labkey.experiment.saveRuns(baseUrl=”http://labkey/”, folderPath=”home”, protocolName=labkey.experiment.SAMPLE_DERIVATION_PROTOCOL, runList=run) # } Run…

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chromoMap function – RDocumentation

Usage chromoMap( ch.files, data.files, title = c(), ch_gap = 5, ploidy = 1, top_margin = 25, left_margin = 50, chr_width = 15, chr_length = 4, chr_color = c(“black”), data_based_color_map = FALSE, segment_annotation = FALSE, lg_x = 0, lg_y = 0, data_type = c(“numeric”, “categorical”), labels = FALSE, canvas_width = NULL,…

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ggplot2loon function – RDocumentation

Examples # NOT RUN { if(interactive()) { p <- ggplot(mtcars, aes(wt, mpg)) + geom_point() g <- ggplot2loon(p) p1 <- ggplot(mtcars) + geom_point(aes(x = wt, y = mpg, colour = factor(gear))) + facet_wrap(~am) g1 <- ggplot2loon(p1) # } # NOT RUN { df <- data.frame( x = rnorm(120, c(0, 2, 4)),…

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multiRegression function – RDocumentation

Examples # NOT RUN { seed = 1234 N = 100 # sample size Ng = 5 # gene number Nk = 5 * 3 # eQTL number Ns = 1 # sparse ratio sigma2 = 0.01 # sigma2 set.seed(seed) data = randomFSSEMdata(n = N, p = Ng, k =…

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labkey.provenance.stopRecording function – RDocumentation

Examples Run in Workspace # NOT RUN { library(Rlabkey) ## object inputs (from an assay run) and material inputs ## oi <- labkey.selectRows(baseUrl=”https://labkey.org/labkey/”, folderPath = “Provenance”, schemaName=”assay.General.titer”, queryName=”Data”, colSelect= c(“LSID”), colFilter=makeFilter(c(“Run/RowId”,”EQUAL”,”253″))) mi <- data.frame(lsid=c(“urn:lsid:labkey.com:Sample.251.MySamples:sample1″, “urn:lsid:labkey.com:Sample.251.MySamples:sample2″)) p <- labkey.provenance.createProvenanceParams(name=”step1″, description=”initial step”, objectInputs=oi[[“LSID”]], materialInputs=mi) r <- labkey.provenance.startRecording(baseUrl=”https://labkey.org/labkey/”, folderPath = “Provenance”, provenanceParams=p) run…

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stri_trans_nfc function – RDocumentation

Unicode Normalization Forms are formally defined normalizations of Unicode strings which, e.g., make possible to determine whether any two strings are equivalent. Essentially, the Unicode Normalization Algorithm puts all combining marks in a specified order, and uses rules for decomposition and composition to transform each string into one of the…

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sqliteCopyDatabase function – RDocumentation

Description Copies a database connection to a file or to another database connection. It can be used to save an in-memory database (created using dbname = “:memory:” or dbname = “file::memory:”) to a file or to create an in-memory database a copy of another database. Usage sqliteCopyDatabase(from, to) Arguments from…

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h2o.explain function – RDocumentation

Description The H2O Explainability Interface is a convenient wrapper to a number of explainabilty methods and visualizations in H2O. The function can be applied to a single model or group of models and returns a list of explanations, which are individual units of explanation such as a partial dependence plot…

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RunPCA function – RDocumentation

RunPCA(object, …) # S3 method for default RunPCA( object, assay = NULL, npcs = 50, rev.pca = FALSE, weight.by.var = TRUE, verbose = TRUE, ndims.print = 1:5, nfeatures.print = 30, reduction.key = “PC_”, seed.use = 42, approx = TRUE, … ) # S3 method for Assay RunPCA( object, assay =…

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Adjust the legends distance to the x-axis?

ggplot2: Adjust the legends distance to the x-axis? I want to shrink the legends distance to the x-axis, but I can’t find a way to do it. Is it possible? Example code: library(ggplot2) ggplot(mtcars, aes(x = gear, y = mpg, fill = gear)) + geom_bar(stat = “identity”) + theme(legend.position =…

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labkey.pipeline.getProtocols function – RDocumentation

Description Gets the protocols that have been saved for a particular pipeline. Usage labkey.pipeline.getProtocols(baseUrl=NULL, folderPath, taskId, path, includeWorkbooks = FALSE) Arguments baseUrl a string specifying the baseUrl for the LabKey server folderPath a string specifying the folderPath taskId a string identifier for the pipeline path a string for the relative…

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labkey.webdav.delete function – RDocumentation

Description This will delete the supplied file or folder under the specified LabKey Server project using WebDAV. Usage labkey.webdav.delete( baseUrl=NULL, folderPath, remoteFilePath, fileSet=”@files” ) Arguments baseUrl a string specifying the baseUrl for the labkey server folderPath a string specifying the folderPath remoteFilePath the path to delete, relative to the LabKey…

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