profileplot {Starr} | R Documentation

## Vizualize clusters

### Description

Visualization of a set of “profiles” (i.e. a consecutive series of measurements like a time series, or the DNA binding levels along different positions on a gene). The profiles are given as the rows of a (samples x positions) matrix that contains the measurements. Instead of plotting a line for each profile (row of the matrix), the q-quantiles for each position (column of the matrix) are calculated, where q runs through a set of representative quantiles. Then for each q, a line of q-quantiles is plotted along the positions. Color coding of the quantile profiles aids the interpretation of the plot: There is a color gradient from the median profile to the 0 (=min) resp. 1(=max) quantile.

### Usage

    profileplot(cluster, label=NULL,	at=NULL, main = "", xlim=NULL, xlab = "", xaxt = "s",xlabels = NULL, las = 1, ylim=NULL, ylab = "", fromto = c(0.05,0.95),colpal = "heat", 	nrcolors = 25, outer.col="light grey", add.quartiles = T, add = F, separate = T)

### Arguments

`cluster` | a (samples x columns) matrix with numerical entries. Each sample row is understood as a consecutive series of measurements. Missing values are not allowed so far
`label` | if multiple clusters should be plotted in one diagram, the cluster labels for each item are given in this vector
`at` | optional vector of length ncol(cluster), default = 1:ncol(cluster). Specifies the x-values at which the positions will be plotted.
`main` | the title of the plot, standard graphics parameter
`xlim` | xlimits, standard graphics parameter
`xlab` | x-axis legend, standard graphics parameter
`xaxt` | should an x axis be plotted at all? (="n" if not), standard graphics parameter
`xlabels` | character vector. If specified, this text will be added at the “at“-positions as x-axis labels.
`las` | direction of the xlabels text. las=1: horizontal text, las=2: vertical text
`ylim` | ylimits, standard graphics parameter
`ylab` | y-axis legend, standard graphics parameter
`fromto` | determines the smallest and the largest quantile that are plotted in colors, more distant values are plotted as outliers
`colpal` | either "red","green","blue" (predefined standard color palettes in profileplot), or a vector of colors to be used instead.
`nrcolors` | not very important. How many colors will the color palette contain? Usually, the default = 25 is sufficient
`outer.col` | color of the outlier lines, default = "light grey". For no outliers, choose outer.col="none"
`add.quartiles` | should the quartile lines be plotted (grey/black)? default=TRUE
`add` | should the profile plot be added to the current plot? Defaults to FALSE
`separate` | should each cluster, be plotted in a separate window? Defaults to TRUE

### Author(s)

Achim Tresch, Benedikt Zacher tresch@lmb.uni-muenchen.de

### Examples

    sampls = 100
    probes = 63
    at = (-31:31)*14
    clus = matrix(rnorm(probes*sampls,sd=1),ncol=probes)
    clus= rbind( t(t(clus)+sin(1:probes/10))+1:nrow(clus)/sampls , t(t(clus)+sin(pi/2+1:probes/10))+1:nrow(clus)/sampls )
    labs = paste("cluster",kmeans(clus,4)$cluster)

    profileplot(clus,main="All data",fromto=c(0,1))
    profileplot(clus,label=labs,main="Clustered data",colpal=c("heat","blue","red","topo"),add.quartiles=FALSE)
    profileplot(clus,main="Same data, 4 clusters in one plot\n color gradient fromto = c(0.4,0.6), no outliers plotted",label=labs,separate=FALSE,xaxt="n",fromto=c(0.4,0.6),
    	colpal=c("heat","blue","red","green"),outer.col="none")

[Package Starr version 1.42.0 Index]