myheatmap: Heatmap

In NBBttest: Negative Binomial Beta t-Test

Heatmap

Description

This function is used to display heatmap of differential expressions of genes or isoforms detected by NBBttest in the real count data.

Usage

myheatmap(dat, IDcol, nci, r, r1, r2, 
colrs="greenred", rwcex=2.0,clcex=2.0,x=10, tree="both",
method="euclidean", ky=1.5, rowBarColor=NULL,  
colBarColor=NULL,  labrow="yes", labcol="yes", rsort="yes",
adjrow=c(0.3, 0.0 ), adjcol = c(1, 1) , rwangle=30,
clangle=30,  maptitle)

Arguments

dat	is NBBttest object that is outputted by mbetattest, includes information columns, data columns, t-value column, pvalue column,selection column.
IDcol	nonnegative int value, indicating which column is ID column where IDs will be shown in heatmap rows, is required.
nci	nonnegative int value,indicating column number of informaction (gene or isoform annotation) columns in the data, is required.
r	nonnegative int value, indicating column number of count data including empty columns if there are multiple datasets with the same row names.
r1	nonnegative int value, indicating replicate number in condition 1.
r2	nonnegative int value, indicating replicate number in cocndition 2.
colrs	heatmap colors. User has 8 options: "redgreen", "greenred", "redblue", "bluered", "cm.colors", "terrain.colors","topo.colors", and"heat.colors".
rwcex	numeric argument: nonnegative value, used as cex.axis in for the row axis labeling.Default=1.8.
clcex	numeric argument: nonnegative value, used as cex.axis for the column axis labeling. Default=1.8.
x	numeric argument: nonnegative value, used as argument of cm.colors(x), terrain.colors(x) and topo.colors(x), the default value is 10.
tree	tree(s) drawn on row or colum or both. User has four options: "both" for drawing trees on both row and column,"row" for drawing tree only on row,"column" for drawing tree only on column, and "none" for no tree specified on rows and columns. Default is "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 is "euclidean".
ky	numeric argument: nonnegative value is used to determine key size. The defalut =1.5
rowBarColor	(optional) character vector for RowSideColors and colRow. Length of rowBarColor equals to gene or isoform number or row number. rowBarColor contains the color names of classes or typpes or groups of row names and show row color side bars and color row names. If row names, for example, genes in row are not classified, then we suggest user use its default value: rowBarColor is NULL.
colBarColor	(optional) character vector for colSideColors and colCol. Length of colBarColor equals to sample number. colBarColor contains the color names of classes or typpes or groups of coloumn names and show column color side bars and color column names. If column names, for example, samples in column are just two types, then we suggest user use its default value: colBarColor=NULL.
labrow	string, logistic value. Rows on heatmap are labeled with genes or targets if labrow="yes", otherwise, the rows are not labeled.
labcol	string, logistical value. columns on heatmap are labeled with samples or treatments if labcol="yes", otherwise, the columns are not labeled.
rsort	logistical value. If choose tree="both" or "row", then rsort does not work. However, if tree ="none" or "columnn", then rsort ="yes" will force rows to be sorted in descent way. The default is "yes"
adjrow	two numeric values. The first value is used to adjust left or right position (x-axis) of labels, and the second value is used to adjust up or down position (y-axis) of labels. The fadault values are c(0.4, 1).
adjcol	two numeric values. The first value is used to adjust left or right position (x-axis) of labels, and the second value is used to adjust up or down position (y-axis) of labels. The fadault values are c(1, 1 ).
rwangle	angle of xlab under heatmap. The Default value is 30.
clangle	angle of ylab. The default value is 30
maptitle	string argument for giving heatmap title, default is set to be empty string ' '.

Details

This function uses sigificance to choose data 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. If r>(r1+r2), then data dat are multiple datasets.

Value

no return value but create a heatmap.

Note

requres gplots and grDevices.

Author(s)

Yuan-De Tan [e-mail]

See Also

heatmap.2, myheatmap2

Examples

 
data(result)
colclass=c("1","1","1","2","2","2")
oldpar <- par(no.readonly =TRUE)
on.exit(par(oldpar))
par(mar=c(7.5,5.5,3.5,1.2))
par(oma=c(3,1,1,3))
myheatmap (dat=result, IDcol=1, nci=7, r=6, r1=3,
r2=3, colrs="terrain.colors", rowBarColor=NULL,  
colBarColor=colclass, labrow="no", labcol="yes", 
rsort="yes", adjrow=c(0.3, 0.0 ), 
adjcol = c(1, 1) , maptitle="My heatmap")

NBBttest documentation built on May 30, 2022, 1:05 a.m.