topSeqsPlot {LymphoSeq} | R Documentation |
Create a cumulative frequency bar plot of a specified number of top sequences.
topSeqsPlot(list, top = 10)
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. |
The plot is made using the package ggplot2 and can be reformatted using ggplot2 functions. See examples below.
Returns a cumulative frequency bar plot of the top sequences.
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/).
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))