plotPCPApp {bigPint}R Documentation

Plot interactive parallel coordinate plots

Description

Plot interactive parallel coordinate plots.

Usage

plotPCPApp(data = data, pointColor = "orange")

Arguments

data

DATA FRAME | Read counts for parallel coordinate lines

pointColor

CHARACTER STRING | Color of overlaid points on scatterplot matrix; default "orange"

Value

A Shiny application that shows a parallel coordinate plot and allows users to draw rectangular areas across samples and remove genes that are not inside these areas. The user can download a file that contains the gene IDs that remain.

Examples

# Example: Create interactive parallel coordinate plot for genes that have
# FDR < 0.01 and logFC < -4. Standardize genes to have an average of zero
# and a standard deviation of one.

data(soybean_ir_sub)
data(soybean_ir_sub_metrics)

# Create standardized version of data
library(matrixStats)
soybean_ir_sub_st = as.data.frame(t(apply(as.matrix(soybean_ir_sub[,-1]), 1,
    scale)))
soybean_ir_sub_st$ID = as.character(soybean_ir_sub$ID)
soybean_ir_sub_st = soybean_ir_sub_st[,c(length(soybean_ir_sub_st),
    1:length(soybean_ir_sub_st)-1)]
colnames(soybean_ir_sub_st) = colnames(soybean_ir_sub)
nID = which(is.nan(soybean_ir_sub_st[,2]))
soybean_ir_sub_st[nID,2:length(soybean_ir_sub_st)] = 0

library(dplyr, warn.conflicts = FALSE)
plotGenes = filter(soybean_ir_sub_metrics[["N_P"]], FDR < 0.01,
    logFC < -4) %>% select(ID)
pcpDat = filter(soybean_ir_sub_st, ID %in% plotGenes[,1])

app <- plotPCPApp(data = pcpDat, pointColor = "purple")
if (interactive()) {
    shiny::runApp(app, display.mode = "normal")
}

[Package bigPint version 1.2.2 Index]