plotDiffTpcaVolcano {Rtpca} | R Documentation |
Plot differential TPCA analysis results
plotDiffTpcaVolcano( tpcaObj, alpha = 0.1, setXLim = FALSE, xlimit = c(-0.75, 0.75) )
tpcaObj |
a tpcaObj after having performed
a differential analysis, see |
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 |
ggplot displaying a volcano plot
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)