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 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']])

[Package ropls version 1.22.0 Index]