geneEmbedPlot {tomoda} | R Documentation

## Embedding plot for genes

### Description

Scatter plot for genes with two-dimenstional embeddings in a `SummarizedExperiment` object. Each point stands for a gene.

### Usage

    geneEmbedPlot(object, gene.df, group = "center", method = "TSNE")

### 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.
`method` | Character, the embeddings for scatter plot. Must be one of `"TSNE"`, `"UMAP"`, or `"PCA"`.

### Value

A `ggplot` object.

### Examples

    data(zh.data)
    zh <- createTomo(zh.data)
    peak_genes <- findPeakGene(zh)
    zh <- runTSNE(zh, peak_genes$gene)
    # Color genes by peak centers.
    geneEmbedPlot(zh, peak_genes)

    # Color genes by peak starts.
    geneEmbedPlot(zh, peak_genes, group="start")

    # Do not color genes.
    geneEmbedPlot(zh, peak_genes["gene"])

[Package tomoda version 1.0.0 Index]