Plotting Module of the 'ribios' Software Suite
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Documentation for package ‘ribiosPlot’ version 1.3.0
Help Pages
| as.data.frame.PCAScoreMatrix | Coerece a PCAScoreMatrix into data.frame |
| as.matrix.PCAScoreMatrix | Coerece a PCAScoreMatrix into score matrix |
| biosHeatmap | CUSTOMED HEATMAP.2 FOR BIOS USERS |
| blackgoldred | Two and three-color panels |
| blackgreen | Two and three-color panels |
| blackred | Two and three-color panels |
| blackredyellow | Two and three-color panels |
| blackwhite | Two and three-color panels |
| blackyellow | Two and three-color panels |
| blueblackred | Two and three-color panels |
| bluered | Two and three-color panels |
| brewer.pal.factor | Build brewer.pal colors from factor (Deprecated) |
| brewer.pal.factorLevels | Build brewer.pal colors from factor (Deprecated) |
| cascadeOrder | Order rows of a matrix in the cascade order |
| closeFileDevice | Open a device as a file preparing for plotting in the file |
| colorpanel | Generates a set of colors that varies smoothly. |
| compactPar | Compact par setting |
| compactTrellis | Return a compact setting for lattice plots, useful for preparing publications |
| confEllipse | Plot confidence ellipse based on two-dimenstional data |
| cyanblackyellow | Two and three-color panels |
| degree2radian | Convert degree to radian values |
| display.colorpanels | Display color panels |
| display.threecolor.panels | Display three-color panels |
| display.twocolor.panels | Display two-color panels |
| ellipse | Add an ellipse in an existing plot |
| expVar | S3 function expVar to extract explained variance from prcomp and PCAScoreMatrix objects |
| expVar.PCAScoreMatrix | S3 function expVar to extract explained variance from prcomp and PCAScoreMatrix objects |
| expVar.prcomp | S3 function expVar to extract explained variance from prcomp and PCAScoreMatrix objects |
| expVarLabel | Generic function expVarLabel to generate a label of explained variance from prcomp and PCAScoreMatrix objects |
| expVarLabel.PCAScoreMatrix | Labels of principal components from PCAScoreMatrix |
| expVarLabel.prcomp | Labels of principal components from prcomp |
| fcbase | Return base colors of a fcol object |
| fcbase<- | Replace base colors of a fcol object with a different value |
| fcbrewer | Factor color brewer |
| fcol | Construct a fcol object |
| figurePanel | Make a figure panel with title |
| getDefaultFontFamily | Get default font family |
| getExpVarLabel | Helper function to print PC and explained variances |
| getLims | Get xlim/ylim ranges for plots from real values |
| ggSmoothScatter | Mimicking the graphics::smoothScatter behaviour for GGally::ggpairs |
| ggSmoothScatterWithAux | Mimicking the graphics::smoothScatter behaviour for GGally::ggpairs, with aux lines |
| greenred | Two and three-color panels |
| guessWH | Guess width and height parameters for a heatmap |
| heat | Two and three-color panels |
| histMat | Make histograms for matrix |
| idev | Interative dev.print and pdf print |
| intRange | Return a range defined by integers |
| ipdf | Interative dev.print and pdf print |
| jitter.xyplot | Make boxplots or dotplots with sample-size proportional jitters |
| magentayellow | Two and three-color panels |
| midCol | Blender two colors to get the midpoint color of two colors |
| nonNull | Make sure that x is assigned a reasonable value |
| openFileDevice | Open a device as a file preparing for plotting in the file |
| p2asterisk | Convert p values into asterisks |
| panel.cor | Correlation panel for pairs |
| panel.lmSmooth | Correlation panel |
| pcaRotation | Retrieve PCA rotations from prcomp objects |
| PCAScoreMatrix | Construct a S3-class PCAScoreMatrix object |
| pcaScores | Retrieve PCA scores from prcomp objects |
| pcaScoresFromLogFC | Perform principal component analysis and derive PCA scores from a logFC matrix |
| pdf2png | Use 'convert' (ImageMagick) to convert PDF to high-quality PNG |
| plotPCA | S3 method plotPCA |
| plotPCA.prcomp | Visualise PCA results of expression data with the sample plot |
| plotPCAloading | Plot PCA loading |
| plotVenn | Plot Venn object of the Vennerable package |
| print.fcol | Print a fcol object |
| print.PCAScoreMatrix | Print PCAScoreMatrix |
| qBreaks | Internal function to re-calculate breaks of histograms when x-axis is clipped |
| qHist | Histogram with quantile line(s) and text(s) |
| radian2degree | Convert radian to degree values |
| redblackblue | Two and three-color panels |
| redblue | Two and three-color panels |
| redgreen | Two and three-color panels |
| robustDist | Robust distance |
| royalbluegrayred | Two and three-color panels |
| royalbluered | Two and three-color panels |
| royalredblue | Two and three-color panels |
| royalredgrayblue | Two and three-color panels |
| setCompactTrellis | Set compact trellis as default |
| squareLayout | Plan a square/matrix layout of plots |
| symrange | Return a symmetric range |
| threecolor.panels | Return available three-color panels |
| turyeb | Two and three-color panels |
| twocolor.panels | Return available three-color panels |
| vennMembersDataframe | Extract members of each region in Venn diagrams in to a data.frame |
| vennMembersList | Extract members of each region in Venn diagrams in to a list |
| whiteblack | Two and three-color panels |
| whiteblue | Two and three-color panels |
| whiteblueblackheat | Two and three-color panels |
| whitered | Two and three-color panels |
| xclipHist | Histogram with clipped x axis |
| yellowblack | Two and three-color panels |
| yellowblackcyan | Two and three-color panels |
| yellowmagenta | Two and three-color panels |
| [.PCAScoreMatrix | Subsetting PCAScoreMatrix while keeping the expVar attribute |