geneCorHeatmap {tomoda} | R Documentation

## Correlation heatmap of genes

### Description

Heatmap of correlation coefficients between any two queried genes in a `SummarizedExperiment` object.

### Usage

    geneCorHeatmap(
      object,
      gene.df,
      group = "center",
      matrix = "scaled",
      size = 5,
      cor.method = "pearson"
    )

### Arguments

`object` | A `SummarizedExperiment` object.
`gene.df` | Data.frame. The first column must be a vector of gene names, and has the name `"gene"`. Additional columns in `gene.df` can be used to set the colors of genes.
`group` | Character, a column name in `gene.df` defining the groups of genes. Genes in the same group have same colors on the side bar.
`matrix` | Character, must be one of `"count"`, `"normalized"`, or `"scaled"`.
`size` | Numeric, the size of gene names. Set it to 0 if you do not want to show gene names.
`cor.method` | Character, the method to calculate correlation coefficients. must be one of `"pearson"`, `"kendall"`, or `"spearman"`.

### Details

This method can create a pure heatmap or a heatmap with side bar. If you prefer a pure heatmap, input a `gene.df` with a single column of gene names. However, you may want to show additional information of genes with a side bar, and the grouping information should be saved as additional column(s) of `gene.df`, and declared as `group`. By default, you can use the output by `findPeakGene` as input `gene.df`. Peak genes will be grouped by their centers on the side bar.

### Value

A `ggplot` object.

### Examples

    data(zh.data)
    zh <- createTomo(zh.data)

    # Correlation heatmap for all peak genes.
    peak_genes <- findPeakGene(zh)
    geneCorHeatmap(zh, peak_genes)

    # Use Spearman correlation coefficients.
    geneCorHeatmap(zh, peak_genes, cor.method="spearman")

    # Group genes by peak start.
    geneCorHeatmap(zh, peak_genes, group="start")

    # Plot without side bar.
    geneCorHeatmap(zh, data.frame(
     gene=c("ENSDARG00000002131", "ENSDARG00000003061", "ENSDARG00000076075", "ENSDARG00000076850")))

[Package tomoda version 1.0.0 Index]