plotMDS: biplot Multidimensional Scaling result

In ph-pham/RepSeq: Analysis of High-throughput sequencing repertoire data (RepSeqTools)

Description

function computes pairwise distances between all libs for a chosen level. Then, multidimentional scaling (2 dimensions) is applied to the resulting matrix, ggplot was used to represente individuals on the scaling dimensions.

Usage

plotMDS(
  x,
  level = c("VpJ", "V", "J", "VJ", "CDR3aa"),
  method = c("manhattan", "euclidean", "canberra", "clark", "bray", "kulczynski",
    "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup", "binomial",
    "chao", "cao", "mahalanobis"),
  colGrp = NULL
)

Arguments

x	an object of class RepSeqExperiment.
level	repertoire level VpJ, V, J, VJ, CDR3aa.
method	distance computation method. Choose one among manhattan, euclidean, canberra, clark, bray, kulczynski, jaccard, gower, altGower, morisita, horn, mountford, raup, binomial, chao, cao, mahalanobis.
colGrp	color by group of samples. A string of character containng the name of the varibale indicating group of samples (must be a column name in the slot sampleData). If NULL, the number of colors is equal to the number of sample.

Value

a dot plot.

Examples

## Not run: 
# The package RepSeqData contains example datasets 
library(RepSeqData)
colnames(sData(RepSeqData))
# plot 2 first axes of multidimensional scaling performed on the dissimilarity matrix.
plotMDS(x = RepSeqData, level = "V", method = "euclidean", colGrp = "project")

## End(Not run)

ph-pham/RepSeq documentation built on Dec. 22, 2021, 7:47 a.m.