R语言热图怎么实现


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cc
heatmap(test,cexCol=0.9,labRow=NA,main = “Heatmap”)heatmap(test, col = cm.colors(256), scale = “column”, RowSideColors = rc, ColSideColors = cc, margins = c(5,10), main = “Heatmap(rainbow color)”)热图(二)– 香港云主机 pheatmaplibrary(pheatmap)annotation_row = data.frame(GeneClass = factor(rep(c(“Path2”, “Path3”, “Path4”), c(10, 4, 6))))annotation_col = data.frame(CellType = factor(rep(c(“CT1”, “CT2”), 5)), Time = 1:5)pheatmap(test,border_color=NA,col=rainbow(nrow(test),start = 0, end = .3),cexCol=0.9,cellwidth = 30,cellheight = 18,main = “Pheatmap”)par(mar=c(5,4,8,10))pheatmap(test,main = ‘Pheatmap’)### add numberspheatmap(test,border_color=NA,col=rainbow(nrow(test),start = 0, end = .3),cexCol=0.9,cellwidth = 30,cellheight = 18,display_numbers=T,main = “Pheatmap”)热图(三)– heatmap.2library(gplots)heatmap.2(test,keysize=1.5,symkey=F,density.info=”none”,trace=”none”,labRow=NA,col=”heat.colors”,main=”heatmap.2″)xval
pal
heatmap.2(test,symkey=F,density.info=”none”,labRow=NA,col=pal,tracecol=”#303030″,trace=”none”,cellnote=xval,notecol=”black”,notecex=0.8,keysize=1.5,main=”heatmap.2″)热图(四)– ggplot2(上、下三角热图)mydata
head(mydata)cormat
head(cormat)library(reshape2)melted_cormat
head(melted_cormat)library(ggplot2)ggplot(data = melted_cormat, aes(x=Var1, y=Var2, fill=value)) +geom_tile()############################### 2# Get lower triangle of the correlation matrixget_lower_tri
cormat[upper.tri(cormat)]
return(cormat)}# Get upper triangle of the correlation matrixget_upper_tri
cormat[lower.tri(cormat)]
return(cormat)}upper_tri
upper_tri# Melt the correlation matrixlibrary(reshape2)melted_cormat
melted_cormat
# Heatmaplibrary(ggplot2)ggplot(data = melted_cormat, aes(Var2, Var1, fill = value))+geom_tile(color = “white”)+scale_fill_gradient2(low = “blue”, high = “red”, mid = “white”,midpoint = 0, limit = c(-1,1), name=”PearsonnCorrelation”) +theme_minimal()+theme(axis.text.x = element_text(angle = 45, vjust = 1,size = 12, hjust = 1))+coord_fixed()################################### 3reorder_cormat
# Use correlation between variables as distancedd
hc
cormat
}# Reorder the correlation matrixcormat
upper_tri
# Melt the correlation matrixmelted_cormat
melted_cormat
# Create a ggheatmapggheatmap
geom_tile(color = “white”)+scale_fill_gradient2(low = “blue”, high = “red”, mid = “white”,midpoint = 0, limit = c(-1,1), name=”PearsonnCorrelation”) +theme_minimal()+ # minimal themetheme(axis.text.x = element_text(angle = 45, vjust = 1,size = 12, hjust = 1))+coord_fixed()# Print the heatmapprint(ggheatmap)########################################4ggheatmap +geom_text(aes(Var2, Var1, label = value), color = “black”, size = 4) +theme(axis.title.x = element_blank(),axis.title.y = element_blank(),panel.grid.major = element_blank(),panel.border = element_blank(),panel.background = element_blank(),axis.ticks = element_blank(),legend.justification = c(1, 0),legend.position = c(0.6, 0.7),legend.direction = “horizontal”)+guides(fill = guide_colorbar(barwidth = 7, barheight = 1,title.position = “top”, title.hjust = 0.5))热图(五)– LDheatmap#source(“http://bioconductor.org/biocLite.R”)#biocLite(“Heatplus”)library(Heatplus)library(LDheatmap)library(combinat)library(genetics)data(CEUData)MyHeatmap
color = grey.colors(20))flippedHeatmap
old.prompt
LDheatmap.highlight(MyHeatmap, i = 3, j = 8, col = “black”, fill = “grey” )# Plot a symbol in the center of the pixel which represents LD between# the fourth and seventh SNPs:LDheatmap.marks(MyHeatmap, 4, 7, gp=gpar(cex=2), pch = “*”)rgb.palette
LDheatmap(MyHeatmap, color=rgb.palette(18))热图(六)–其他a) 系统树颜色data
head(data)sig
data1
#rownames(data1)
#data3
library(gplots)library(“devtools”)my_palette
heatmap.2(data1,keysize=1.5,symkey=F,denscol=tracecol,density.info=”none”,trace=”none”,scale=”row”,dendrogram =”row”,labRow=NA,col=my_palette,margins = c(8,8))#data2
#source(“http://bioconductor.org/biocLite.R”)#biocLite(“Heatplus”) # annHeatmap or annHeatmap2data2
my_palette
library(Heatplus)library(permute)library(vegan)library(RColorBrewer)library(gplots)data.dist
row.clus
var1
var1
var1
#cbind(row.names(data2), var1)data.dist.g
col.clus
#heatmap.2(data2,Rowv = as.dendrogram(row.clus),Colv = as.dendrogram(col.clus), col = my_palette,RowSideColors = var1, margins = c(10, 3))heatmap.2(data2, Rowv = as.dendrogram(row.clus),Colv = as.dendrogram(col.clus), col = my_palette,RowSideColors = var1, margins = c(11, 5), trace = “none”,density.info = “none”, xlab = “genera”, ylab = “Samples”,main = “Heatmap example”, lhei = c(2, 8))#plot(annHeatmap2(data2,col = colorRampPalette(c(“Magenta”,”Goldenrod3″,”SpringGreen3″),space = “rgb”)(61), breaks = 50,dendrogram = list(Row = list(dendro = as.dendrogram(row.clus)),Col = list(dendro = as.dendrogram(col.clus))), legend = 3,labels = list(Col = list(nrow = 12))))plot(annHeatmap2(data2, col = colorRampPalette(c(“Magenta”,”Goldenrod3″,”SpringGreen3″),space = “rgb”)(61), breaks = 50, dendrogram = list(Row = list(dendro = as.dendrogram(row.clus)),Col = list(dendro = as.dendrogram(col.clus))),legend = 3, labels = list(Col = list(nrow = 6)),ann = list(Row = list(data = ann.dat))))ann.dat
var2 = rnorm(nrow(data2), mean = 50, sd = 20))plot(annHeatmap2(data2, col = colorRampPalette(c(“Magenta”,”Goldenrod3″,”SpringGreen3″),space = “rgb”)(61), breaks = 50, dendrogram = list(Row = list(dendro = as.dendrogram(row.clus)),Col = list(dendro = as.dendrogram(col.clus))),legend = 3, labels = list(Col = list(nrow = 6)),ann = list(Row = list(data = ann.dat)),cluster = list(Row = list(cuth = 0.76, col = brewer.pal(4, “Set2”)))))热图(六)–其他b) 注释信息library(MASS)library(pheatmap)library(RColorBrewer)sim.expr.data
n1 = n – n0times = 1:p # used for creating covariance matrixH
V0
V1
# rows are people, columns are genesgenes0
genes1
genes
return(genes)}n = 100 ; n0 = 50 ; n1 = 50; p = 100genes
rho.0 = 0.01, rho.1 = 0.95)colnames(genes)
rownames(genes)
genes[1:5, 1:5]# RColorBrewer::display.brewer.all()col.pal
annotation_col
Exposure = factor(c(rep(“X=0”,n0), c(rep(“X=1”, n1)))),Type = factor(sample(c(“T-cell”,”B-cell”),n, replace=T)))rownames(annotation_col) = paste0(“Subject”, 1:n)head(annotation_col)annotation_row
Pathway = factor(rep(1:4,each=25)))rownames(annotation_row) = paste0(“Gene”, 1:n)head(annotation_row)pheatmap::pheatmap(t(genes),cluster_row = T,cluster_cols = F,annotation_col = annotation_col,annotation_row = annotation_row,color = col.pal,fontsize = 6.5,fontsize_row=6,fontsize_col = 6,gaps_col=50)热图(六)–其他c) triple heatmaplibrary(ggplot2);library(reshape2)library (grid)#X axis quantitaive ggplot datadatfx
levels =rev(paste(“ID”, 1:20, sep = “”))), matrix(sample(LETTERS[1:7],80, T), ncol = 4))# converting data to long form for ggplot2 usedatf1x
plotx
colour = “white”) + scale_fill_manual(values= terrain.colors(7))+ scale_x_discrete(expand=c(0,0))px
#Y axis quantitaive ggplot datadatfy
levels =rev(paste(“ID”,21:40, sep = “”))), matrix(sample(LETTERS[7:10],100, T), ncol = 5))# converting data to long form for ggplot2 usedatf1y
ploty
colour = “white”) + scale_fill_manual(values= c(“cyan4”, “midnightblue”, “green2”, “lightgreen”)) + scale_x_discrete(expand=c(0,0))py
)# plot XY quantative filldatfxy
levels =rev(paste(“ID”, 1:20, sep = “”))), matrix(rnorm (400, 50, 10), ncol = 20))names (datfxy)
datfxy
levels (datfxy$ variable)
pxy
colour = “white”) + scale_fill_gradient(low=”red”, high=”yellow”) + theme(axis.title=element_blank())#Define layout for the plots (2 rows, 2 columns)layt
#View the layout of plotsgrid.show.layout(layt)#Draw plots one by one in their positionsgrid.newpage()pushViewport(viewport(layout=layt))print(py,vp=viewport(layout.pos.row=1,layout.pos.col=1))print(pxy,vp=viewport(layout.pos.row=1,layout.pos.col=2))print(px,vp=viewport(layout.pos.row=2,layout.pos.col=2))以上就是关于“R语言热图怎么实现”这篇文章的内容,相信大家都有了一定的了解,希望小编分享的内容对大家有帮助,若想了解更多相关的知识内容,请关注开发云行业资讯频道。

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