BI_heatmap.dds2: a quick way to draw heatmap

In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

Description

a quick way to draw heatmap.heatmap.dds2 is a plus version of heatmap.dds.

Usage

heatmap.dds2(dds,
             transformation = "normTransform",
             expr.matrix = NULL,log.convert = T,
             select,
             design,
             contrast.col,
             contrast.level=NULL,
             contrast.list,
             rowscale=T,
             expr.name = "expression",
             cluster_rows = T,cluster_cols=T,
             row.k = 4,
             show_column_names = F,
             show_row_names = T,
             clustering_distance_row = "euclidean",
             clustering_distance_column = "euclidean",
             column_names_gp = gpar(fontsize = 16, fontface = "bold"),
             row_names_gp = gpar(fontsize = 16, fontface = "bold"))

Arguments

dds	dds object.IF NULL,expr.matrix should provide expression matrix.
transformation	normTransform or vst
expr.matrix	If NULL,dds object gives the expression matrix.
log.convert	whether do a log scale
select	select markers or genes
design	a design object
contrast.col	the colnames of contrast
contrast.level	If NULL,use default level.
contrast.list	a specified list.see example.
rowscale	whether scaling and centering of matrix-like objects
expr.name	a legend name of expression data
cluster_rows,cluster_cols	whether cluster in row or col direction
row.k	the number of annotated color in row direction
show_column_names,show_row_names	whether to show column or row names
clustering_distance_row	see ComplexHeatmap::Heatmap
clustering_distance_column	see ComplexHeatmap::Heatmap
column_names_gp	see ComplexHeatmap::Heatmap and the example
row_names_gp	see ComplexHeatmap::Heatmap and the example

Value

heatmap plot

Author(s)

Weibin Huang

See Also

ComplexHeatmap::Heatmap() lucky::heatmap.dds()

Examples

data(expr) #use internal data "expr" in lucky package.
dds=NULL
transformation = "normTransform"
expr.matrix=expr[,1:(ncol(expr)-3)]
select=c("gene1","gene2","gene3","gene4","gene5","gene6")
design=data.frame(condition=Fastextra(colnames(exprs.matirx),"_",2),
                  condition1=Fastextra(colnames(exprs.matirx),"_",2),
                  row.names = colnames(exprs.matirx))
contrast.col="condition"
contrast.list=list(condition = c("cell01" = "green",
                                 "cell02" = "gray",
                                 "cell03" = "darkred"),
                   condition1 = c("cell01" = mycolor[1],
                                  "cell02" = mycolor[2],
                                  "cell03" = mycolor[3]))
expr.name = "exprs"
heatmap.dds2(dds=NULL,
             transformation=NULL,
             expr.matrix,
             log.convert=F,
             select,design,
             contrast.col,contrast.level=NULL,
             contrast.list,
             rowscale=T,
             expr.name,
             cluster_rows=T,cluster_cols=T,
             row.k=2,
             show_column_names=T,show_row_names=T)

## example:the setting of contrast.list of continuous value
library(circlize)
col = list(
 cyl = c("4" = "green", "6" = "gray", "8" = "darkred"),
 am = c("0" = "yellow","1" = "orange"),
 mpg = colorRamp2(c(17, 25), c("lightblue", "purple"))
)

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.