plotFCPseudocolor {TCC} | R Documentation

## Create a pseudo-color image of simulation data

### Description

This function creates a pseudo-color image of simulation data regarding the number of differentially expressed genes (DEGs) and the breakdowns for individual groups from a TCC-class object.

### Usage

    plotFCPseudocolor(tcc, main, xlab, ylab)

### Arguments

`tcc` | TCC-class object.
`main` | character string indicating the plotting title.
`xlab` | character string indicating the x-label title.
`ylab` | character string indicating the y-label title.

### Details

This function should be used after the `simulateReadCounts` function that generates simulation data with arbitrary defined conditions. The largest log fold-change (FC) values are in magenta and no-changes are in white.

### Examples

    # Generating a simulation data for comparing two groups
    # (G1 vs. G2) with biological replicates.
    # the first 200 genes are DEGs, where 180 are up in G1.
    tcc <- simulateReadCounts(Ngene = 1000, PDEG = 0.2,
                              DEG.assign = c(0.9, 0.1),
                              DEG.foldchange = c(4, 4),
                              replicates = c(3, 3))
    plotFCPseudocolor(tcc)

    # Generating a simulation data for comparing three groups
    # (G1 vs. G2 vs. G3) with biological replicates.
    # the first 300 genes are DEGs, where the 70%, 20%, and 10% are
    # up-regulated in G1, G2, G3, respectively. The levels of DE are
    # 3-, 10, and 6-fold in individual groups.
    tcc <- simulateReadCounts(Ngene = 1000, PDEG = 0.3,
                              DEG.assign = c(0.7, 0.2, 0.1),
                              DEG.foldchange = c(3, 10, 6),
                              replicates = c(3, 3, 3))
    plotFCPseudocolor(tcc)

[Package TCC version 1.28.0 Index]