view {ropls} | R Documentation |
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
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" )
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 |
this method has no output
this method has no output
this method has no output
This function has no output.
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']])