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Last data update: 2014.03.03

R: Heatmap

myheatmap

R Documentation

Heatmap

Description

This function is used to display heatmap of differential expressions of genes or isoforms or differential splicings of genes detected by the multiple beta t-test method in the real data.

Usage

myheatmap(dat, r1, r2, W, colrs, tree, method, rwangle, clangle, maptitle)

Arguments

`dat`	data outputted by mbeta_ttest, includes information columns, data columns, t-value, rho and symbol columns;
`r1`	numeric argument: number of replicate libraries in condition 1.
`r2`	numeric argument: number of replicate libraries in condition 2
`W`	numeric argument: threshold for choosing genes or isoforms for heatmap. W value can be set to be 0 to any large number. If you set W =0, then the function will select all differentially expressed genes with symb="+". To choose a appropriate W, user needs to refere to rho values in the result file. Default W=1.
`colrs`	heatmap colors. User has 5 options: "redgreen", "greenred", "redblue", "bluered" and "heat.colors". Default colrs="redgreen".
`tree`	object of heatmap. User has four options: "both" for row and column trees,"row" for only row tree,"column" for only column tree, and "none" for no tree specified. Default tree="both".
`method`	method to be chosen to calculate distance between columns or rows. It has four options: "euclidean", "pearson","spearman" and "kendall". The latter three are d=1-cc where cc is correlation coefficients. Default="euclidean".
`rwangle`	angle of xlab under heatmap. Default value is 30.
`clangle`	angle of ylab. Default value is 30
`maptitle`	string for heatmap title.

Details

This function uses W (omega) and symb to choose genes or isoforms in the data ordered by t-values and then to normalize the selected data by using z-scale. This function has multiple options to select map color, distance, cluster and x- and y-lab angles. The heatmap was designed for publication and presentation, that is, zoom of the figure can be reduced without impacting solution.

Value

no return value but create a heatmap.

Note

myheatmap requres gplots

Author(s)

Yuan-De Tan tanyuande@gmail.com

Examples

require(gplots)
data(dat) 

#dat<-mbetattest(X=jkttcell,na=3,nb=3,W=1,alpha=0.05,
#file="C:/mBeta_ttest/R_package/jurkat_NS_48h_tag_mbetattest.csv")

# data(mtcars)
#x  <-as.matrix(mtcars)
#myheatmap(dat=x,r1=3,r2=3, maptitle="mtcars_heatmap")
 
myheatmap(dat=dat,r1=3,r2=3,maptitle="Jurkat T-cell heatmap2")

myheatmap(dat=dat,r1=3,r2=3,tree="none",maptitle="Jurkat T-cell heatmap")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MBttest)
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: gtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MBttest/myheatmap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: myheatmap
> ### Title: Heatmap
> ### Aliases: myheatmap
> ### Keywords: heatmap
> 
> ### ** Examples
> 
> require(gplots)
> data(dat) 
> 
> #dat<-mbetattest(X=jkttcell,na=3,nb=3,W=1,alpha=0.05,
> #file="C:/mBeta_ttest/R_package/jurkat_NS_48h_tag_mbetattest.csv")
> 
> # data(mtcars)
> #x  <-as.matrix(mtcars)
> #myheatmap(dat=x,r1=3,r2=3, maptitle="mtcars_heatmap")
>  
> myheatmap(dat=dat,r1=3,r2=3,maptitle="Jurkat T-cell heatmap2")
> 
> myheatmap(dat=dat,r1=3,r2=3,tree="none",maptitle="Jurkat T-cell heatmap")
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>