GSEPD_PCA_Plot {rgsepd} | R Documentation

## Principle Components Analysis figure generation

### Description

After processing the pipeline, users may want to have further PCA figures generated. This function takes a completed GSEPD object and generates informative figures, based on the differentially expressed genes.

### Usage

    GSEPD_PCA_Plot(GSEPD, customColors=FALSE)

### Arguments

`GSEPD` | The master object, it should have already been run through GSEPD_Process().
`customColors` | a boolean value, when FALSE, default behavior is to color points to match the test conditions. When TRUE, use sampleMeta$CustomColor column for a sample-by-sample user specification. This behavior disables the built-in legend.

### Value

No return value. Generates files.

### See Also

GSEPD_PCA_Spec

### Examples

      data("IlluminaBodymap")
      data("IlluminaBodymapMeta")
      set.seed(1000) #fixed randomness
      isoform_ids <- Name_to_RefSeq(c("HIF1A","EGFR","MYH7","CD33","BRCA2"))
      rows_of_interest <- unique( c( isoform_ids ,
                                     sample(rownames(IlluminaBodymap),
                                            size=2000,replace=FALSE)))
      G <- GSEPD_INIT(Output_Folder="OUT",
                    finalCounts=round(IlluminaBodymap[rows_of_interest , ]),
                    sampleMeta=IlluminaBodymapMeta,
                    COLORS=c("green","black","red"))
      G <- GSEPD_ChangeConditions( G, c("A","B")) #set testing groups first!
      G <- GSEPD_Process( G ) #have to have processed results to plot them
      GSEPD_PCA_Plot(G)

[Package rgsepd version 1.19.1 Index]