plotDiffTpcaVolcano: Plot differential TPCA analysis results

In nkurzaw/Rtpca: Thermal proximity co-aggregation with R

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)

nkurzaw/Rtpca documentation built on May 12, 2023, 2:10 p.m.