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]