Skip to contents

Visualization of the inter-repertoire sharing on a scatter plot

Source: R/plotFunctions.R
plotScatter.Rd

This function computes a correlation between a pair of repertoires at any repertoire level. It allows a comparative analysis of the occurrence of a given repertoire level between a pair of samples, which goes beyond the simple calculation of the sharing degree.

Usage

plotScatter(
  x,
  sampleNames = NULL,
  level = c("aaClone", "ntClone", "V", "J", "VJ", "ntCDR3", "aaCDR3"),
  scale = c("frequency", "count", "log"),
  shiny = FALSE
)

Arguments

x

an object of class RepSeqExperiment

sampleNames

a vector of character indicating the two sample_ids of the repertoires to be analyzed.

level

a character specifying the level of the repertoire to be analyzes. Should be one of "aaClone", "ntClone", "V", "J", "VJ", "ntCDR3" or "aaCDR3".

scale

a character specifying whether to plot in "count" , "frequency". or "log'

shiny

default is FALSE. whether to plot the shiny compatible version

Examples


data(RepSeqData)
plotScatter(x = RepSeqData,
            level = "V",
            sampleNames = c("tripod-30-813", "tripod-30-815", "tripod-31-846"),
            scale = "log")
#> Warning: log-10 transformation introduced infinite values.
#> Warning: log-10 transformation introduced infinite values.
#> Warning: log-10 transformation introduced infinite values.
#> Warning: log-10 transformation introduced infinite values.
#> Warning: log-10 transformation introduced infinite values.
#> Warning: log-10 transformation introduced infinite values.

            
plotScatter(x = RepSeqData,
            level = "aaClone",
            sampleNames = c("tripod-30-813", "tripod-30-815"),
            scale = "frequency")
#> Warning: Ignoring unknown parameters: `label.fontface`
#> `geom_smooth()` using formula = 'y ~ x'