Repertoire dynamics

# S3 method for immunr_dynamics
vis(.data, .plot = c("smooth", "area", "line"), .order = NA, .log = F, ...)

Arguments

.data

Output from the trackClonotypes function.

.plot

Character. Either "smooth", "area" or "line". Each specifies a type of plot for visualisation of clonotype dynamics.

.order

Numeric or character vector. Specifies the order to samples, e.g., it used for ordering samples by timepoints. Either See "Examples" below for more details.

.log

Logical. If TRUE then use log-scale for the frequency axis.

...

Not used here.

Examples

if (FALSE) { # Load an example data that comes with immunarch data(immdata) # Option 1 # Choose the first 10 amino acid clonotype sequences # from the first repertoire to track tc = trackClonotypes(immdata$data, list(1, 10), .col = "aa") # Choose the first 20 nucleotide clonotype sequences # and their V genes from the "MS1" repertoire to track tc = trackClonotypes(immdata$data, list("MS1", 20), .col = "nt+v") # Option 2 # Choose clonotypes with amino acid sequences "CASRGLITDTQYF" or "CSASRGSPNEQYF" tc = trackClonotypes(immdata$data, c("CASRGLITDTQYF", "CSASRGSPNEQYF"), .col = "aa") # Option 3 # Choose the first 10 clonotypes from the first repertoire # with amino acid sequences and V segments target = immdata$data[[1]] %>% select(CDR3.aa, V.name) %>% head(10) tc = trackClonotypes(immdata$data, target) # Visualise the output regardless of the chosen option # Therea are three way to visualise it, regulated by the .plot argument vis(tc, .plot = "smooth") vis(tc, .plot = "area") vis(tc, .plot = "line") # Visualising timepoints # First, we create an additional column in the metadata with randomly choosen timepoints: immdata$meta$Timepoint = sample(1:length(immdata$data)) immdata$meta # Next, we create a vector with samples in the right order, according to the "Timepoint" column (from smallest to greatest): sample_order = order(immdata$meta$Timepoint) # Sanity check: timepoints are following the right order: immdata$meta$Timepoint[sample_order] # Samples, sorted by the timepoints: immdata$meta$Sample[sample_order] # And finally, we visualise the data: vis(tc, .order = sample_order) }