heatmapPEI {cogena} | R Documentation

## heatmap of the gene set enrichment from a cogena object.

### Description

heatmap of the gene set enrichment score. After obtaining the ennrichemt of clusters for each gene set, the heatmapPEI will show it as a heatmap in order. The value shown in heatmapPEI is the -log2(fdr), representing the enrichment score.

### Usage

    heatmapPEI(
      object,
      method,
      nCluster,
      CutoffNumGeneset = 20,
      CutoffPVal = 0.05,
      orderMethod = "max",
      roundvalue = TRUE,
      low = "grey",
      high = "red",
      na.value = "white",
      maintitle = NULL,
      printGS = FALSE,
      add2 = TRUE,
      geom = "tile",
      wrap_with = 40
    )

    ## S4 method for signature 'cogena'
    heatmapPEI(
      object,
      method = clusterMethods(object),
      nCluster = nClusters(object),
      CutoffNumGeneset = 20,
      CutoffPVal = 0.05,
      orderMethod = "max",
      roundvalue = TRUE,
      low = "grey",
      high = "red",
      na.value = "white",
      maintitle = NULL,
      printGS = FALSE,
      add2 = TRUE,
      geom = "tile",
      wrap_with = 60
    )

### Arguments

`object` | a genecl or cogena object
`method` | as clMethods in genecl function
`nCluster` | as nClust in cogena function.
`CutoffNumGeneset` | the cut-off of the number of gene sets in the return table
`CutoffPVal` | the cut-off of p-value. The default is 0.05.
`orderMethod` | the order method, default is max, other options are "mean", "all", "I", "II" or a number meaning the ith cluster.
`roundvalue` | The default is TRUE. whether or not round the data. such as round(1.54, 1)=1.5
`low` | colour for low end of gradient.
`high` | colour for high end of gradient.
`na.value` | Colour to use for missing values.
`maintitle` | a character. like GSExxx. the output of figure will like "cogena: kmeans 3 GSExxx" in two lines. Default is NULL
`printGS` | print the enriched gene set names or not. Default is FALSE
`add2` | enrichment score for add Up and Down reuglated genes.
`geom` | tile or circle
`wrap_with` | default 40. wrap strings

### Details

The x-axis shows cluster i and the number of genes in cluster, with red means cluster containing up-regulated genes, green means down-regulated genes, black means there are up and down regulated genes in this cluster and blue means all DEGs. If parameter add2 is true, another two columns will be shown as well, representing the up and down regulated genes.

The direction of DEGs are based on latter Vs former from sample labels. For example, labels are as.factor(c("ct", "Disease")), the "Disease" are latter compared with "ct". Usually, the order is the alphabet.

The y-axis represents the gene sets enriched.

orderMethod:

- max. ordered by the max value in clusters beside all

- mean. ordered by the mean value in clusters beside all

- All. ordered by all genes

- Up. ordered by up-regulated genes (add2 should be TRUE)

- Down. ordered by down-regulated genes (add2 should be TRUE)

### Value

a gene set enrichment heatmap

### See Also

`clEnrich` and `heatmapCluster`

### Examples

    data(Psoriasis)
    annofile <- system.file("extdata", "c2.cp.kegg.v7.01.symbols.gmt.xz",
    package="cogena")

    ## Not run:
    genecl_result <- coExp(DEexprs, nClust=2:3, clMethods=c("hierarchical","kmeans"),
        metric="correlation", method="complete", ncore=2, verbose=TRUE)

    clen_res <- clEnrich(genecl_result, annofile=annofile, sampleLabel=sampleLabel)

    #summay this cogena object
    summary(clen_res)

    #heatmapPEI
    heatmapPEI(clen_res, "kmeans", "2")
    heatmapPEI(clen_res, "kmeans", "2", orderMethod="mean")
    heatmapPEI(clen_res, "kmeans", "3", CutoffNumGeneset=20,
        low = "#132B43", high = "#56B1F7", na.value = "grey50")

    ## End(Not run)

[Package cogena version 1.28.0 Index]