plotTpcaVolcano: Plot TPCA analysis results

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

Plot TPCA analysis results

Description

Plot TPCA analysis results

Usage

plotTpcaVolcano(tpcaObj, alpha = 0.1)

Arguments

tpcaObj	a tpcaObj after having performed a differential analysis, see runDiffTPCA
alpha	significance level / FDR at which null hypothesis should be rejected

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
)

complex_anno <- tibble(
    protein = c("3", "4", "5", 
       "4", "5", "6", "7"),
    id = c(rep("1", 3), rep("2", 4)),
    count = c(rep(3, 3), rep(4, 4)))

tpca_result <- runTPCA(
  mat_list, complexAnno = complex_anno)

plotTpcaVolcano(tpca_result)

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