plotDiffTpcaVolcano {Rtpca} | R Documentation

## Plot differential TPCA analysis results

### Description

Plot differential TPCA analysis results

### Usage

    plotDiffTpcaVolcano(
      tpcaObj,
      alpha = 0.1,
      setXLim = FALSE,
      xlimit = c(-0.75, 0.75)
    )

### Arguments

`tpcaObj` | a tpcaObj after having performed a differential analysis, see `runDiffTPCA`
`alpha` | significance level / FDR at which null hypothesis should be rejected
`setXLim` | logical determining whether x-axis limits should be set according to xlimit
`xlimit` | numeric vector with two elements determing the x-axis limits, only is implemented if setXLim is set to TRUE

### Value

ggplot displaying a volcano plot

### Examples

    library(dplyr)
    library(Biobase)

    m1 <- matrix(1:28, ncol = 4)
    m2 <- matrix(2:25, ncol = 4)
    m3 <- matrix(c(2:10, 1:19), ncol = 4)

    rownames(m1) <- 1:7
    rownames(m2) <- 3:8
    rownames(m3) <- 2:8

    mat_list <- list(
        m1, m2, m3
    )

    c1 <- matrix(29:2, ncol = 4)
    c2 <- matrix(26:3, ncol = 4)
    c3 <- matrix(c(11:3, 20:2), ncol = 4)

    rownames(c1) <- 1:7
    rownames(c2) <- 3:8
    rownames(c3) <- 2:8

    contrast_list <- list(
        c1, c2, c3
    )

    ppi_anno <- tibble(
        x = c("3", "3"),
        y = c("5", "7"),
        pair = c("3:5", "3:7"))

    ref_df <- tibble(
        pair = c("3:5", "3:7"),
        valueC2 = c(4, 8)
    )

    diff_tpca <- runDiffTPCA(
      mat_list, contrast_list, ppiAnno = ppi_anno)

    plotDiffTpcaVolcano(diff_tpca)

[Package Rtpca version 1.2.0 Index]