view: view

In ropls: PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data

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 method has no output

this method has no output

This function has no output.

See Also

str, view

image, view

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']])

ropls documentation built on Nov. 8, 2020, 7:46 p.m.