simplexplot {debCAM} | R Documentation

## The plot of scatter simplex

### Description

This function shows scatter simplex of mixture expressions.

### Usage

    simplexplot(data, A, MGlist = NULL, data.extra = NULL,
      corner.order = NULL, col = "gray", pch = 1, cex = 0.8,
      mg.col = "red", mg.pch = 1, mg.cex = 1.2, ex.col = "black",
      ex.pch = 19, ex.cex = 1.5, ...)

### Arguments

`data` | A data set that will be internally coerced into a matrix. Each row is a gene and each column is a sample. Data should be in non-log linear space with non-negative numerical values (i.e. >= 0). Missing values are not supported. All-zero rows will be removed internally.
`A` | Prior/Estimated proportion matrix.
`MGlist` | A list of vectors, each of which contains known markers and/or CAM-detected markers for one subpopulation.
`data.extra` | Extra data points to be shown in the simplex plot, e.g. the points associated with prior/estimated proportion vectors. The format should be consistent with `data`, so prior/estimated proportion matrix needs to be transposed before as the input.
`corner.order` | The order to show simplex corners counterclockwise.
`col` | The color for data points. The default is "gray".
`pch` | The symbol/character for data points. The default is 1.
`cex` | The symbol/character expansion for data points. The default is 0.8.
`mg.col` | The colors for marker genes. Marker genes of one subpopulation could have their own color if a vector is provided. The default is "red".
`mg.pch` | The symbols/characters for marker genes. Marker genes of one subpopulation could have their own symbol/character if a vector is provided. The default is 1.
`mg.cex` | The symbol/character expansion for marker genes. The default is 1.2.
`ex.col` | The colors for extra data points. Each data point could have its own color if a vector is provided. The default is "black".
`ex.pch` | The symbols/characters for extra data points. Each data point could have its own symbol/character if a vector is provided. The default is 19.
`ex.cex` | The symbol/character expansion for extra data points. The default is 1.5.
`...` | All other arguments are passed to the plotting command.

### Details

This function can show the scatter simplex and detected marker genes in a 2D plot. The corners in the high-dimensional simplex will still locate at extreme points of low-dimensional simplex. These corners will follow the order set by `corner.order` to display in the plot counterclockwise.

### Value

A plot to the current device.

### Examples

    #obtain data, A matrix, marker genes
    data(ratMix3)
    data <- ratMix3$X
    A <- ratMix3$A
    pMGstat <- MGstatistic(ratMix3$S, c("Liver","Brain","Lung"))
    pMGlist.FC <- lapply(c("Liver","Brain","Lung"), function(x)
        rownames(pMGstat)[pMGstat$idx == x & pMGstat$OVE.FC > 10])

    #plot simplex for data
    simplexplot(data, A)
    simplexplot(data, A, MGlist = pMGlist.FC) #Color marker genes in the plot
    simplexplot(data, A, MGlist = pMGlist.FC,
        data.extra = t(A)) #show the location of proportion vectors in the plot

    #set different corner order and colors
    simplexplot(data, A, MGlist = pMGlist.FC, corner.order = c(2,1,3),
                col = "blue", mg.col = c("red","orange","green"))

[Package debCAM version 1.4.0 Index]