heatmap.3: More customized heatmap that allow control over color key

In Liuy12/MBDDiff: MBDDiff for processing MBDcap-seq datasets

Description

More customized heatmap that is designed based on heatmap.2 that gives user control over color key

Usage

heatmap.3(Exprs, sel = FALSE, thres_mean, thres_var, numbreaks = 100, col = c("blue", "white", "red"), breakratio = c(2, 1, 2), colsidebar, Colv = FALSE, Rowv = TRUE, scale = "row", labRow = FALSE, labCol = FALSE, dendrogram = "row")

Arguments

Exprs	A numeric matrix or data.frame
sel	Whether you want to pre-filter the genes first based on average expression and variance
thres_mean	If 'sel' is set to TRUE, what threshold you wanna use for average expression
thres_var	If 'sel' is set to TRUE, what threshold you wanna use for variance
numbreaks	The number of breaks for colorkey. Default to 100
col	A vector of length 3 of colors you want to use for colorkey. Default to c("blue", "white", "red")
breakratio	How you wanna the colorkey to be partitioned according to the colors.
colsidebar	Whether you want to add a column side bar above the heatmap
Colv	Logical value indicating whether you want to perform clustering on columns
Rowv	Logical value indicating whether you want to perform clustering on rows
scale	Whether you want to scale the input matrix row-wise or column wise so that each row or column has mean equals to 0 and variance equals to 1. Possible values are 'row' and 'column'
labRow	Logical value indicating whether you want to label rows based on row names of input matrix
labCol	Logical value indicating whether you want to label columns based on column names of input matrix
dendrogram	One of values in "both", "row", "column", "none". Indicating how you wanna the dendrogram to be drawn

Details

heatmap.3 internally calls heatmap.2 from gplots package, which uses layout to arragent the plot elements. Consequentially, it can not be used in a multi column/row layout using layout(...), par(mfrow=...) or (mfcol=...).

Author(s)

Yuanhang Liu

References

https://github.com/Liuy12/MBDDiff

See Also

heatmap.2

Examples

    data(PromoterCount)
    heatmap.3(as.matrix(Promoter[1:100,]))

Liuy12/MBDDiff documentation built on May 7, 2019, 2 p.m.