imatplot: Create Interactive Line Plots

In aoles/iSVGplots: Interactive SVG plots in R

Description

Plots interactive SVG line charts.

Usage

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
         ...)  

Arguments

data	data.frame containing data to be plotted, where each column corresponds to one line
metadata	data.frame containing metadata associated with individual lines
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 matplot.

Details

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.

Author(s)

Andrzej Oles, [e-mail]

Examples

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" )

aoles/iSVGplots documentation built on May 10, 2019, 12:42 p.m.