R: Plots sequence logo as a layer on ggplot

geom_logo {ggseqlogo} | R Documentation

## Plots sequence logo as a layer on ggplot

### Description

Plots sequence logo as a layer on ggplot

### Usage

    geom_logo(data = NULL, method = "bits", seq_type = "auto",
      namespace = NULL, font = "roboto_medium", stack_width = 0.95,
      rev_stack_order = F, col_scheme = "auto", low_col = "black",
      high_col = "yellow", na_col = "grey20", plot = T, ...)

### Arguments

`data` | Character vector of sequences or named list of sequences. All sequences must have same width.
`method` | Height method, can be one of "bits" or "probability" (default: "bits")
`seq_type` | Sequence type, can be one of "auto", "aa", "dna", "rna" or "other" (default: "auto", sequence type is automatically guessed)
`namespace` | Character vector of single letters to be used for custom namespaces. Can be alphanumeric, including Greek characters.
`font` | Name of font. See `list_fonts` for available fonts.
`stack_width` | Width of letter stack between 0 and 1 (default: 0.95)
`rev_stack_order` | If `TRUE`, order of letter stack is reversed (default: FALSE)
`col_scheme` | Color scheme applied to the sequence logo. See `list_col_schemes` for available fonts. (default: "auto", color scheme is automatically picked based on `seq_type`). One can also pass custom color scheme objects created with the `make_col_scheme` function
`low_col, high_col` | Colors for low and high ends of the gradient if a quantitative color scheme is used (default: "black" and "yellow").
`na_col` | Color for letters missing in color scheme (default: "grey20")
`plot` | If `FALSE`, plotting data is returned
`...` | Additional arguments passed to layer params

### Examples

    # Load sample data
    data(ggseqlogo_sample)

    # Produce single sequence logo using geom_logo
    p1 = ggseqlogo( seqs_dna[[1]] )

[Package ggseqlogo version 0.1 Index]