1. pcaExplorer
  2. man
  3. pcaplot3d.Rd
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adding anchors of package names in function calls of the docs

Federico Marini authored on 19/12/2024 20:48:32
Showing 1 changed files
man/pcaplot3d.Rd
History View file @ 9c694b2
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@@ -18,9 +18,9 @@ pcaplot3d(
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 )
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 }
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 \arguments{
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-\item{x}{A \code{\link[=DESeqTransform]{DESeqTransform()}} object, with data in \code{assay(x)},
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-produced for example by either \code{\link[=rlog]{rlog()}} or
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-\code{\link[=varianceStabilizingTransformation]{varianceStabilizingTransformation()}}}
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+\item{x}{A \code{\link[DESeq2:DESeqTransform]{DESeq2::DESeqTransform()}} object, with data in \code{assay(x)},
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+produced for example by either \code{\link[DESeq2:rlog]{DESeq2::rlog()}} or
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+\code{\link[DESeq2:varianceStabilizingTransformation]{DESeq2::varianceStabilizingTransformation()}}}
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 \item{intgroup}{Interesting groups: a character vector of
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 names in \code{colData(x)} to use for grouping}
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markdownified roxygen blocks

Federico Marini authored on 12/09/2024 13:07:22
Showing 1 changed files
man/pcaplot3d.Rd
History View file @ e63fe6d
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@@ -18,9 +18,9 @@ pcaplot3d(
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 )
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 }
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 \arguments{
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-\item{x}{A \code{\link{DESeqTransform}} object, with data in \code{assay(x)},
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-produced for example by either \code{\link{rlog}} or
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-\code{\link{varianceStabilizingTransformation}}}
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+\item{x}{A \code{\link[=DESeqTransform]{DESeqTransform()}} object, with data in \code{assay(x)},
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+produced for example by either \code{\link[=rlog]{rlog()}} or
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+\code{\link[=varianceStabilizingTransformation]{varianceStabilizingTransformation()}}}
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 \item{intgroup}{Interesting groups: a character vector of
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 names in \code{colData(x)} to use for grouping}
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Updated man after linting

Federico Marini authored on 20/01/2020 23:05:29
Showing 1 changed files
man/pcaplot3d.Rd
History View file @ c8e298c
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@@ -50,7 +50,7 @@ A html-based visualization of the 3d PCA plot
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 Plots the results of PCA on a 3-dimensional space, interactively
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 }
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 \examples{
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-dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3,betaSD_tissue = 1)
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+dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3, betaSD_tissue = 1)
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 rlt <- DESeq2::rlogTransformation(dds)
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-pcaplot3d(rlt, ntop=200)
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+pcaplot3d(rlt, ntop = 200)
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 }
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updated to newer roxygen version

Federico Marini authored on 18/11/2019 13:17:27
Showing 1 changed files
man/pcaplot3d.Rd
History View file @ 8fa4a88
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@@ -4,9 +4,18 @@
4 4 
 \alias{pcaplot3d}
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 \title{Sample PCA plot for transformed data}
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 \usage{
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-pcaplot3d(x, intgroup = "condition", ntop = 500, returnData = FALSE,
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-  title = NULL, pcX = 1, pcY = 2, pcZ = 3, text_labels = TRUE,
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-  point_size = 3)
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+pcaplot3d(
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+  x,
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+  intgroup = "condition",
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+  ntop = 500,
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+  returnData = FALSE,
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+  title = NULL,
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+  pcX = 1,
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+  pcY = 2,
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+  pcZ = 3,
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+  text_labels = TRUE,
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+  point_size = 3
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+)
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 }
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 \arguments{
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 \item{x}{A \code{\link{DESeqTransform}} object, with data in \code{assay(x)},
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added demo data via button, edited news and bumped version to 2.1.3

Federico Marini authored on 06/04/2017 22:25:18
Showing 1 changed files
man/pcaplot3d.Rd
History View file @ 393dd17
... ... 
@@ -45,4 +45,3 @@ dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3,betaSD_tissue = 1)
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 rlt <- DESeq2::rlogTransformation(dds)
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 pcaplot3d(rlt, ntop=200)
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 }
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-
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further completing the docu

Federico Marini authored on 24/06/2016 15:51:51
Showing 1 changed files
man/pcaplot3d.Rd
History View file @ d42f986
... ... 
@@ -13,6 +13,9 @@ pcaplot3d(x, intgroup = "condition", ntop = 500, returnData = FALSE,
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 produced for example by either \code{\link{rlog}} or
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 \code{\link{varianceStabilizingTransformation}}}
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+\item{intgroup}{Interesting groups: a character vector of
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+names in \code{colData(x)} to use for grouping}
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+
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 \item{ntop}{Number of top genes to use for principal components,
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 selected by highest row variance}
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... ... 
@@ -30,11 +33,16 @@ selected principal components and intgroup covariates for custom plotting}
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 \item{text_labels}{Logical, whether to display the labels with the sample identifiers}
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 \item{point_size}{Integer, the size of the points for the samples}
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-
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-\item{Interesting}{groups: a character vector of
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-names in \code{colData(x)} to use for grouping}
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+}
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+\value{
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+A html-based visualization of the 3d PCA plot
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 }
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 \description{
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 Plots the results of PCA on a 3-dimensional space, interactively
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 }
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+\examples{
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+dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3,betaSD_tissue = 1)
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+rlt <- DESeq2::rlogTransformation(dds)
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+pcaplot3d(rlt, ntop=200)
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+}
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completing documentation for future R CMD check and co

Federico Marini authored on 24/06/2016 15:22:52
Showing 1 changed files
man/pcaplot3d.Rd
History View file @ 4a1e5b3
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new file mode 100644
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@@ -0,0 +1,40 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/pcaplot.R
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+\name{pcaplot3d}
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+\alias{pcaplot3d}
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+\title{Sample PCA plot for transformed data}
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+\usage{
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+pcaplot3d(x, intgroup = "condition", ntop = 500, returnData = FALSE,
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+  title = NULL, pcX = 1, pcY = 2, pcZ = 3, text_labels = TRUE,
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+  point_size = 3)
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+}
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+\arguments{
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+\item{x}{A \code{\link{DESeqTransform}} object, with data in \code{assay(x)},
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+produced for example by either \code{\link{rlog}} or
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+\code{\link{varianceStabilizingTransformation}}}
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+
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+\item{ntop}{Number of top genes to use for principal components,
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+selected by highest row variance}
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+
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+\item{returnData}{logical, if TRUE returns a data.frame for further use, containing the
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+selected principal components and intgroup covariates for custom plotting}
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+
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+\item{title}{The plot title}
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+
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+\item{pcX}{The principal component to display on the x axis}
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+
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+\item{pcY}{The principal component to display on the y axis}
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+
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+\item{pcZ}{The principal component to display on the z axis}
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+
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+\item{text_labels}{Logical, whether to display the labels with the sample identifiers}
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+
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+\item{point_size}{Integer, the size of the points for the samples}
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+
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+\item{Interesting}{groups: a character vector of
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+names in \code{colData(x)} to use for grouping}
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+}
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+\description{
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+Plots the results of PCA on a 3-dimensional space, interactively
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+}
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+