topSeqsPlot {LymphoSeq} | R Documentation

## Cumulative frequency bar plot of top sequences

### Description

Create a cumulative frequency bar plot of a specified number of top sequences.

### Usage

    topSeqsPlot(list, top = 10)

### Arguments

`list` | A list data frames imported using the LymphoSeq function readImmunoSeq or productiveSeq.
`top` | The number of top sequences to be colored in the bar plot. All other, less frequent sequences are colored violet.

### Details

The plot is made using the package ggplot2 and can be reformatted using ggplot2 functions. See examples below.

### Value

Returns a cumulative frequency bar plot of the top sequences.

### See Also

An excellent resource for examples on how to reformat a ggplot can be found in the R Graphics Cookbook online (http://www.cookbook-r.com/Graphs/).

### Examples

    file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")

    file.list <- readImmunoSeq(path = file.path)

    topSeqsPlot(list = file.list, top = 10)

    # Display the number of sequences at the top of bar plot and add a title
    n <- as.character(lapply(file.list, nrow))

    topSeqsPlot(list = file.list, top = 10) +
       ggplot2::annotate("text", x = 1:length(file.list), y = 105, label = n, color = "black") +
       ggplot2::expand_limits(y = c(0, 110)) + ggplot2::ggtitle("Figure Title") +
       ggplot2::scale_x_discrete(limits = names(file.list))

[Package LymphoSeq version 1.12.0 Index]