linePlot {tomoda} | R Documentation

## Line plot for expression traces

### Description

Plot expression traces for genes across sections in a `SummarizedExperiment` object.

### Usage

    linePlot(object, genes, matrix = "normalized", facet = FALSE, span = 0.3)

### Arguments

`object` | A `SummarizedExperiment` object.
`genes` | A character vector of gene names for plotting expression traces.
`matrix` | Character, must be one of `"count"`, `"normalized"`, or `"scaled"`.
`facet` | Logical. Plot the expression trace of each gene in a facet if it is `TRUE`.
`span` | Numeric, the amount of smoothing for the default loess smoother. Smaller numbers produce wigglier lines, larger numbers produce smoother lines. Set it to 0 for non-smoothing lines.

### Value

A `ggplot` object.

### See Also

`geom_smooth` for plotting smooth lines, `facet_wrap` for faceting genes.

### Examples

    data(zh.data)
    zh <- createTomo(zh.data)
    linePlot(zh,
     c("ENSDARG00000002131", "ENSDARG00000003061", "ENSDARG00000076075", "ENSDARG00000076850"))

    # Do not smooth lines.
    linePlot(zh,
     c("ENSDARG00000002131", "ENSDARG00000003061", "ENSDARG00000076075", "ENSDARG00000076850"), span=0)

    # Plot genes in different facets.
    linePlot(zh,
     c("ENSDARG00000002131", "ENSDARG00000003061", "ENSDARG00000076075", "ENSDARG00000076850"),
     facet=TRUE)

[Package tomoda version 1.0.0 Index]