vis_public_frequencies | R Documentation |
Visualise public clonotype frequencies.
vis_public_frequencies( .data, .by = NA, .meta = NA, .type = c("boxplot", "none", "mean") )
.data |
Public repertoire - an output from the pubRep function. |
.by |
Pass NA if you want to plot samples without grouping. You can pass a character vector with one or several column names from ".meta" to group your data before plotting. In this case you should provide ".meta". You can pass a character vector that exactly matches the number of samples in your data, each value should correspond to a sample's property. It will be used to group data based on the values provided. Note that in this case you should pass NA to ".meta". |
.meta |
A metadata object. An R dataframe with sample names and their properties, such as age, serostatus or hla. |
.type |
Character. Either "boxplot" for plotting distributions of frequencies, "none" for plotting everything, or "mean" for plotting average values only. |
A ggplot2 object.
data(immdata) immdata$data <- lapply(immdata$data, head, 500) pr <- pubRep(immdata$data, .verbose = FALSE) vis(pr, "freq", .type = "boxplot") vis(pr, "freq", .type = "none") vis(pr, "freq", .type = "mean") vis(pr, "freq", .by = "Status", .meta = immdata$meta)
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