debrowser (version 1.0.8)

plot_pca: plot_pca

Description

Plots the PCA results for the selected dataset.

Usage

plot_pca(x = NULL, pcx = 1, pcy = 2, explained = NULL, metadata = NULL, color = NULL, shape = NULL, size = NULL, factors = NULL)

Arguments

x,

dataframe with data

pcx,

x axis label

pcy,

y axis label

explained,

additional axis data

metadata,

additional data

color,

color for plot

shape,

shape for plot

size,

size of the plot

factors,

factors of the plot

Value

pca list

Examples

    load(system.file("extdata", "demo", "demodata.Rda",
            package="debrowser"))
    pca_data<-run_pca(getNormalizedMatrix(
            demodata[rowSums(demodata[,2:7])>10,2:7]))
    metadata<-cbind(colnames(demodata[,2:7]), 
            c(rep("Cond1",3), rep("Cond2",3)))
    colnames(metadata)<-c("samples", "conditions")

    a <- plot_pca(pca_data$PCs, explained = pca_data$explained,
            metadata = metadata, color = "samples",
            size = 5, shape = "conditions",
            factors = c("samples", "conditions"))