Description Usage Arguments Details Author(s) Examples
Plots interactive SVG line charts.
1 2 3 4 5 6 7 | imatplot(data, metadata = rownames(data), grouping = seq(nrow(data)), outdir = getwd(), file = NULL,
palette = c("rgb(255,128,0)", "rgb(255,0,0)", "rgb(255,0,128)", "rgb(255,0,255)", "rgb(128,0,255)", "rgb(0,0,255)", "rgb(0,128,255)", "rgb(0,255,255)"),
hlwd = 2, opacity = 1.0,
# passed to svg device
width = 7, height = 7, pointsize = 12,
# passed to matplot
...)
|
data |
|
metadata |
|
grouping |
the grouping of the data |
outdir |
output directory; dafaults to current working directory. |
file |
a character string giving the output file name; if it is NULL, then no external file is created and the drawing occurs on screen. |
palette |
colors used for highlighting groups. |
hlwd |
highlighted line width. |
opacity |
onmouseover line opacity. |
width, |
the width and height of the graphics region in inches. The default values are 7. |
height |
|
pointsize |
the point size to be used; defaults to 12. |
... |
arguments passed to |
imatplot
uses the matplot
function for drawing. Plots are then garnished and exported to SVG
using the SVGAnnotation
package.
Use Google Chrome browser for best viewing experience.
Andrzej Oles, andrzej.oles@embl.de
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | data(data)
df = as.data.frame(exprs(data))
metadata = fData(data)
points = c("tsc03PS_tu1", "tsc03PS_18w1r", "tsc03PS_6w1r", "tsc01PS_48h", "tsc03PS_6w2r", "tsc03PS_18w2r", "tsc03PS_tu2" )
samples = 1:2000 #dim(data)[1]
## this will be our input to the plotting function
d = df[samples, points] + 1e-7
m = metadata[samples, c("Gene.Symbol", "Entrez.Gene.ID")]
targets = m$Gene.Symbol
## do the plotting
imatplot(data = d,
metadata = m,
grouping = targets,
file = "imatplot.svg",
hlwd = 3,
pointsize = 10,
# these are passed to matplot:
lty="solid",
col = c( "#a0a0a005", "#FF0000b0", "#3030FFb0", "#FF30FFb0" )[ (d[, "tsc03PS_18w2r"]>.01)*2 + (d[, "tsc03PS_18w1r"]>.01) + 1 ],
main="TSC03", xlab="",
ylab="log2 norm count",
#xaxt="n",
log="y" )
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