chromoMap (version 0.1)

chromoMap: render interactive chromosome plots

Description

render an interactive graphics of human chromosome. It creates an HTML widget that calls the JavaScript library chromoMap.js that generates the chromosome graphics

required for creating widgets

Usage

chromoMap(chData, type = c("annotation", "heatmap-single", "heatmap-double"),
  align = "horizontal", bgCol = "white", bgBorder = "white",
  chCol = "#c70039", chBorder = "#c70039", annoColor = "orange",
  textCol = "black", HeatColRange = c("red", "white", "blue"),
  dim = c(640, 480), width = NULL, height = NULL)

Arguments

chData

The chromosome data required for annotating chromosome and creating heatmaps. It is a data.frame with atleast three colums viz. name (specify the name for annotation), chrom (specify chromosome name), and start (specify the start position of element). While for heatmaps additional columns data and/or secondData need to added.

type

Specify the type of chromosome plot.Takes only one value from "annotation" , "heatmap-single", or "heatmap-double". For more information about the type of plots see vignette.

align

specify the alignment of plot. Takes the value "horizontal" or "vertical".

bgCol

specify the backround color.

bgBorder

specify the border color.

chCol

specify the body color of chromosomes

chBorder

specify the border color of chromosomes

annoColor

specify the color of annotation bars on the chromosomes.

textCol

specify the text color.

HeatColRange

specify the heat-colors for the heatmap. Takes a character vecter with three color values each corresponding to minimum, medium, and maximum data.

dim

specify dimension of plot. Takes two values for width and height of the plot.

width

use to define width of widget. Usually ignore and do not change

height

height of widget. ignore

Examples

# NOT RUN {
library(chromoMap)
data("pancandata")
#dataset contains two data
#view data set
head(pancandata$data1)
head(pancandata$data2)

#plotting simple annotation
chromoMap(pancandata$data1)

#plotting heatmap-single
chromoMap(pancandata$data1,type="heatmap-single")

#plotting heatmap double
chromoMap(pancandata$data2,type="heatmap-double")

#change orientation of plot
chromoMap(pancandata$data1,align="vertical")

#change chromosome color
chromoMap(pancandata$data1,chCol="green",chBorder="green")

#change chromosome plot background and text color
chromoMap(pancandata$data2,type="heatmap-double",textCol="white",bgCol="black")





# }