heatmapCmap {cogena} | R Documentation

## heatmap designed for for CMap gene set only

### Description

heatmapCmap is desgined for the cogena result from CMap only so as to collapse the multi-isntance drugs in CMap!

### Usage

    heatmapCmap(
      object,
      method = clusterMethods(object),
      nCluster = nClusters(object),
      orderMethod = "max",
      MultiInstance = "drug",
      CutoffNumGeneset = 20,
      CutoffPVal = 0.05,
      mergeMethod = "mean",
      low = "grey",
      high = "red",
      na.value = "white",
      maintitle = NULL,
      printGS = FALSE,
      add2 = TRUE,
      geom = "tile"
    )

    ## S4 method for signature 'cogena'
    heatmapCmap(
      object,
      method = clusterMethods(object),
      nCluster = nClusters(object),
      orderMethod = "max",
      MultiInstance = "drug",
      CutoffNumGeneset = 20,
      CutoffPVal = 0.05,
      mergeMethod = "mean",
      low = "grey",
      high = "red",
      na.value = "white",
      maintitle = "cogena",
      printGS = FALSE,
      add2 = TRUE,
      geom = "tile"
    )

### Arguments

`object` | a genecl or cogena object
`method` | as clMethods in genecl function
`nCluster` | as nClust in cogena function.
`orderMethod` | the order method, default is max, other options are "mean", "all", "I", "II" or a number meaning the ith cluster.
`MultiInstance` | merge multi instances. Options are "drug", "celldrug", "conccelldrug", "concdrug".
`CutoffNumGeneset` | the cut-off of the number of gene sets in the return table. The default is 20.
`CutoffPVal` | the cut-off of p-value. The default is 0.05.
`mergeMethod` | max or mean. The default is mean.
`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. 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

### Details

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)

MultiInstance:

- drug. merge based on cmap_name

- celldrug. merge based on cmap_name and cell type

- conccelldrug. merge based on cmap_name, cell type and concentration

### Value

a gene set enrichment heatmap

### Examples

    data(Psoriasis)
    annofile <- system.file("extdata", "CmapDn100.gmt.xz", package="cogena")
    ## Not run:
    genecl_result <- coExp(DEexprs, nClust=3, clMethods=c("pam"),
        metric="correlation", method="complete", ncore=2, verbose=TRUE)
    clen_res1 <- clEnrich(genecl_result, annofile=annofile, sampleLabel=sampleLabel)

    heatmapCmap(clen_res1, "pam", "3", orderMethod="2")
    heatmapCmap(clen_res1, "pam", "3", orderMethod="2", MultiInstance="concdrug")

    ## End(Not run)

[Package cogena version 1.26.0 Index]