wrGraph: profileAsClu – R documentation

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profileAsClu

Plot profile(s) according to CLustering

Description

This function was made for visualuzing the result of clustering of a numeric vector or clustering along multiple columns of a matrix. The data will be plotted like a reglar scatter-plot, but some extra space is added to separate clusters and dashed lines highlight cluster-borders. If no mean/representative value is spacified, a geometric mean will be calculated along all columns of dat. In case dat has multiple columns, a legend and a representative (default geometric mean) dashed grey line will be displayed.

Usage

profileAsClu(
  dat,
  clu,
  meanD = NULL,
  tit = NULL,
  col = NULL,
  pch = NULL,
  xlab = NULL,
  ylab = NULL,
  meCol = "grey",
  meLty = 1,
  meLwd = 1,
  legLoc = "bottomleft",
  silent = TRUE,
  callFrom = NULL
)

Arguments

`dat`	(matrix or data.frame) main input with data to plot as points
`clu`	(numeric or character) clustering results; if length=1 and character this term will be understood as colum-name with cluster-numbers from `dat`
`meanD`	(numeric) mean/representative of multiple series for display as lines; if length=1 and character this term will be understood as columname with cluster-numbers from `dat`
`tit`	(character) optional custom title
`col`	(character) custom colors
`pch`	(integer) custom plotting symbols (see also `par`)
`xlab`	(character) custom x-axis label
`ylab`	(character) custom y-axis label
`meCol`	(character) color for (dashed) line of mean/representative values
`meLty`	(integer) line-type line of mean/representative values (see also `lty` in `par`)
`meLwd`	(numeric) line-width line of mean/representative values (see also `lwd` in `par`)
`legLoc`	(character) legend location
`silent`	(logical) suppress (less important) messages
`callFrom`	(character) allow easier tracking of message(s) produced

Value

plot only

Examples

set.seed(2020); dat1 <- runif(12)/2 + rep(6:8, each=4)
dat1Cl <- stats::kmeans(dat1, 3)$cluster
dat1Cl <- 5- dat1Cl              # bring cluster-numbers in ascending form
dat1Cl[which(dat1Cl >3)] <- 1    # bring cluster-numbers in ascending form
profileAsClu(dat1, clu=dat1Cl)

wrGraph

Graphics in the Context of Analyzing High-Throughput Data

v1.2.3

GPL-3

Authors

Wolfgang Raffelsberger [aut, cre]

Initial release