The function takes numeric data associated with genes, then performs a smoothing using bins and plots the resulting smoothed signal.
1 2 3 4 5 6 | 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. |
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