R: view

view {ropls}

R Documentation

view

Description

Numeric and graphical display of exprs, pData and fData slots from an ExpressionSet object

Numeric and graphical display of a data frame

Numeric and graphical display of a matrix

Display of the class, mode, size and first...last values from the object; used inside the 'view' wrapper method

Wrapper of the stats::image function used inside the 'view' method

Usage

view(x, ...)

## S4 method for signature 'ExpressionSet'
view(
  x,
  printL = TRUE,
  plotL = TRUE,
  mainC = "",
  paletteC = c("heat", "revHeat", "grey", "revGrey", "palette", "ramp")[1],
  rowAllL = FALSE,
  rowCexN = 1,
  rowMarN = 5.1,
  rowLabC = "",
  rowTruncI = 0,
  colAllL = FALSE,
  colCexN = 1,
  colMarN = 1.1,
  colLabC = "",
  colTruncI = 0,
  drawScaleL = TRUE,
  delimitReplicatesL = FALSE,
  standardizeL = FALSE,
  fig.pdfC = "interactive"
)

## S4 method for signature 'data.frame'
view(
  x,
  printL = TRUE,
  plotL = TRUE,
  mainC = "",
  subC = "",
  paletteC = c("heat", "revHeat", "grey", "revGrey", "palette", "ramp")[1],
  rowAllL = FALSE,
  rowCexN = 1,
  rowMarN = 5.1,
  rowLabC = "",
  rowTruncI = 0,
  colAllL = FALSE,
  colCexN = 1,
  colMarN = 1.1,
  colLabC = "",
  colTruncI = 0,
  drawScaleL = TRUE,
  delimitReplicatesL = FALSE,
  standardizeL = FALSE,
  fig.pdfC = "interactive"
)

## S4 method for signature 'matrix'
view(
  x,
  printL = TRUE,
  plotL = TRUE,
  mainC = "",
  subC = "",
  paletteC = c("heat", "revHeat", "grey", "revGrey", "palette", "ramp")[1],
  rowAllL = FALSE,
  rowCexN = 1,
  rowMarN = 5.1,
  rowLabC = "",
  rowTruncI = 0,
  colAllL = FALSE,
  colCexN = 1,
  colMarN = 1.1,
  colLabC = "",
  colTruncI = 0,
  drawScaleL = TRUE,
  delimitReplicatesL = FALSE,
  standardizeL = FALSE,
  fig.pdfC = "interactive"
)

strF(tableMF, borderI = 2, bigMarkC = ",")

imageF(
  x,
  mainC = "",
  subC = "",
  paletteC = c("heat", "revHeat", "grey", "revGrey", "palette", "ramp")[1],
  rowAllL = FALSE,
  rowCexN = 1,
  rowMarN = 5.1,
  rowLabC = "",
  rowTruncI = 0,
  colAllL = FALSE,
  colCexN = 1,
  colMarN = 1.1,
  colLabC = "",
  colTruncI = 0,
  drawScaleL = TRUE,
  delimitReplicatesL = FALSE,
  standardizeL = FALSE,
  fig.pdfC = "interactive"
)

Arguments

`x`	matrix to be viewed
`...`	Currently not used.
`printL`	should the numerical summary be printed?
`plotL`	should the graphical image be displayed?
`mainC`	character: plot main title
`paletteC`	character: color palette; either 'heat' [default], 'revHeat', 'grey', 'revGrey', 'palette', 'ramp'
`rowAllL`	logical: should all rownames be displayed or only the first and last ones?
`rowCexN`	numeric: size of row labels [default: 1]
`rowMarN`	numeric: row margin [default: 6.1]
`rowLabC`	character: label for the y (row) axis
`rowTruncI`	integer: number of character for truncation of rownames (default, 0, means no truncation)
`colAllL`	logical: should all column names be displayed or only the first and last ones?
`colCexN`	numeric: size of column labels [default: 1]
`colMarN`	numeric: column margin [default: 6.1]
`colLabC`	character: label for the x (column) axis
`colTruncI`	integer: number of character for truncation of colnames (default, 0, means no truncation)
`drawScaleL`	logical: should the color scale be drawn? [default: TRUE]
`delimitReplicatesL`	logical: should lines be added to the image to delimit replicates in row or column names?
`standardizeL`	Logical: should columns be standardized for display? (i.e. subtracting the mean and dividing by the standard deviation) [default: FALSE]
`fig.pdfC`	character: either 'interactive' [default] or the name of the pdf file to save the figure
`subC`	character: plot subtitle
`tableMF`	Input matrix, dataframe or vector
`borderI`	Number of border (first and last) rows and columns to display
`bigMarkC`	Big mark separator for summary results

Value

this method has no output

This function has no output.

Examples

library(ropls)
data(sacurine)
sacSet <- Biobase::ExpressionSet(assayData = t(sacurine[["dataMatrix"]]), 
                                 phenoData = new("AnnotatedDataFrame", 
                                                 data = sacurine[["sampleMetadata"]]), 
                                 featureData = new("AnnotatedDataFrame", 
                                                   data = sacurine[["variableMetadata"]]),
                                 experimentData = new("MIAME", 
                                                      title = "sacurine"))
view(sacSet)
library(ropls)
data(sacurine)
view(sacurine[["sampleMetadata"]])
library(ropls)
data(sacurine)
dataMN <- sacurine[["dataMatrix"]]
view(dataMN)
view(dataMN[, 1:40], mainC = "'Sacurine' dataset", rowAllL = TRUE,
colAllL = TRUE, colTruncI = 13, colMarN = 7)
view(dataMN[, 1:40], mainC = "'Sacurine' dataset", paletteC = "ramp")
sacSet <- Biobase::ExpressionSet(assayData = t(sacurine[["dataMatrix"]]), 
                                 phenoData = new("AnnotatedDataFrame", 
                                                 data = sacurine[["sampleMetadata"]]), 
                                 featureData = new("AnnotatedDataFrame", 
                                                   data = sacurine[["variableMetadata"]]),
                                 experimentData = new("MIAME", 
                                                      title = "sacurine"))
view(sacSet)

data(sacurine)
strF(sacurine[['dataMatrix']])
strF(sacurine[['sampleMetadata']])


data(sacurine)
imageF(sacurine[['dataMatrix']])