myheatmap: Heatmap

Description Usage Arguments Details Value Note Author(s) See Also Examples

View source: R/myheatmap.R

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

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

Arguments

dat

data outputted by mbetattest, 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 user sets 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 [email protected]

See Also

heatmap.2

Examples

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#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")

Yuande/MBttest documentation built on April 29, 2018, 8:05 a.m.