gene expression data

Description Usage Arguments

The function takes numeric data associated with genes, then performs a smoothing using bins and plots the resulting smoothed signal.

E3PlotSmoothGenomeOverview(fcdata, gene.positions = NULL,
  categories = list(All = colnames(fcdata)), label.chr = c(),
  chrlens = NULL, heatcols = c("#00ffff", "#ff00ff"), seg.rescale = 2,
  seg.resolution = 5e+06, seg.hlab = 0.3, seg.vlab = 1e+06,
  legend = NULL, axes.labels = NULL, Rcss = "default",
  Rcssclass = "diamond")

`fcdata`	- numeric matrix with gene/feature names in rownames and samples in colnames. This data will be log2 transformed before the plotting takes place
`gene.positions`	- data frame linking gene names to gene positions
`categories`	- named list of vectors, splitting samples into groups (e.g. Plates or batches). This object also determines the order of the samples on the y axis
`label.chr`	- names of chromosomes to label on horizontal axis (
`chrlens`	- named vector with lengths of chromosomes (chromosomes will appear in this order)
`heatcols`	- numeric vector of lengths two. Determines the color scale of the plot.
`seg.rescale`	- numeric. Used to modulate color intensity
`seg.resolution`	- numeric. Width of bins to use for smoothing
`seg.hlab`	- numeric. Determines spacing between labels near x axis.
`seg.vlab`	- numeric. Determines spacing between labels near y axis.
`legend`	- numeric. Values to use on the legend box.
`axes.labels`	- character vector of length two. Text to write near y axis to the left and to the right of the heatmap.
`Rcss`	- Rcss object. Used to style the heatmap with Rcssplot.
`Rcssclass`	- character vector. Classes to tune Rcssplot formatting.