表型相关热图
library(ComplexHeatmap)
pheatmap(data,scale = "row")
##表达矩阵2个rho和p，需要转为长数据
library(ggcor)
dap <- cor_tbl(p,cluster = T)
darho <- cor_tbl(rho,cluster = T)
pvalue <- quickcor(dap,circular = T,cluster = T,
open = 45, # 缺口大小
# 内圈外圈比例
outer = 0.5,inner = 1.5) +
# 单元格边框线颜色
geom_colour(colour = 'white') +
# 自定义填充颜色
scale_fill_gradient2(low = 'blue',mid = 'white',high = 'red') +
# 基因名
set_p_yaxis() + ##bcols = rand_color(10)+颜色
# 样本名
set_p_xaxis() +
# 更改图例名称
guides(fill = guide_colorbar(title = 'P value')) +
anno_hc_bar(k = 2,fill = rand_color(2),pos = 'top',height = 0.3) +
anno_hc_bar(k = 3,fill = rand_color(3),pos = 'top',height = 0.5) +
anno_hc_bar(k = 4,fill = rand_color(5),pos = 'top',height = 0.2) +
# 添加聚类树
anno_col_tree(bcols = rand_color(5),height = 0.15) +
anno_hc_bar(k = 15,fill = rand_color(15),pos = 'left',width = 0.5) +
anno_hc_bar(k = 10,fill = rand_color(10),pos = 'left',width = 0.5) +
anno_row_tree(bcols = rand_color(8))
# 添加热图
p9 <- quickcor(da,circular = T,cluster = T,grid.colour = 'white',
open = 45, # 缺口大小
# 内圈外圈比例
outer = 2,inner = 1) +
# 单元格边框线颜色
geom_colour(colour = 'white') +
# 自定义填充颜色
scale_fill_gradient2(low = 'blue',mid = 'white',high = 'red',name = 'log2FC') +
# 更改图例名称
# guides(fill = guide_colorbar(title = 'log2FC')) +
# 列注释
anno_hc_bar(k = 2,fill = rand_color(2),pos = 'top',height = 0.3) +
anno_hc_bar(k = 3,fill = rand_color(3),pos = 'top',height = 0.5) +
anno_hc_bar(k = 4,fill = rand_color(5),pos = 'top',height = 0.2) +
# 添加聚类树
anno_col_tree(bcols = rand_color(5),height = 0.15) +
anno_hc_bar(fill = rand_color(15),pos = 'left',width = 0.5) +
anno_hc_bar(k = 10,fill = rand_color(10),pos = 'left',width = 0.5) +
anno_row_tree(bcols = rand_color(8)) +
# 样本名
set_p_xaxis(bcols = rand_color(5))
p9 + anno_row_heat(da,aes(fill = r),width = 0.8,
geom = 'tile') +
scale_fill_gradient2(low = 'green',mid = 'white',high = 'red',name = 'expression') +
# 基因名
set_p_yaxis()# 添加点
p9 + anno_row_heat(da,aes(color = r),width = 0.8,
geom = 'point') +
scale_color_gradient2(low = '#F9B208',mid = 'white',high = '#F55C47',name = 'expression') +
# 基因名
set_p_yaxis()library(OmicCircos)
该包中有两个会用到的函数，一个是segAnglePo(), 该函数能够将基因组片段位置转换成环形弧度，返回一个数据框，用来说明环的大小、片段数量和片段长度。
另一个函数是circos()，用来画不同形状的环，如散点图环、线状图环、热力图环等等。
library(OmicCircos)
2、制作底图信息数据框
首先要有一个数据框（如下，my_contig）来说明你要画的环形图的基本信息，比如基因片段名称、大小等。如下格式
scale_fill_gradient2(low="#445393", high="#EE2627", mid="white")library(tidyverse)
library('ComplexHeatmap')
library('circlize')
library(dendextend)
library(dendsort)
mycol=colorRamp2(c(-1.7, 0.3, 2.3),c( "blue", "white", "red"))##设置颜色scale
circos.clear()
circos.par(gap.after=c(50)) ##circos.par调整圆环首尾间的距离，数值越大，距离越宽
circos.heatmap(data,
col=mycol,
dend.side= "inside", ##聚类树方向，也可outside
track.height = 0.38,##轨道的高度，数值越大圆环越粗
rownames.side= "outside", rownames.col= "black", rownames.cex=0.2, rownames.font=1,##矩阵行名方向
cluster=F, ##是否聚类
dend.track.height=0.18, ##行聚类树高度
dend.callback=function(dend,m,si) { #聚类树回调，dend：当前扇区的树状图；m：当前扇区对应的子矩阵；si：当前扇区的名称
color_branches(dend,k=15,col=1:15) ##聚类树颜色
})
lg=Legend(title= "Exp",col_fun=mycol,direction = c( "vertical"))##图例
grid.draw(lg)
#circos.heatmap内只能是一个矩阵，但如果矩阵数据存在分组，可以用split参数来指定分类变量
split= sample(letters[1:2], 40, replace = TRUE)
split= factor(split, levels = letters[1:2])
circos.heatmap(data,split=split）
#假设有两个热图的矩阵数据
data2=data2
circos.heatmap(data2, col = mycol,rownames.side= "inside",rownames.cex=0.8)
library(gridBase)
lg_Exp1=Legend(title= "Exp1",col_fun=mycol2,direction = c( "vertical"))
lg_Exp2=Legend(title= "Exp2",col_fun=mycol,direction = c( "vertical"))
circle_size= unit(0.07, "snpc")
h= dev.size
lgd_list= packLegend(lg_Exp1,lg_Exp2, max_height = unit(2*h, "inch"))
draw(lgd_list, x = circle_size, just = "left")ggplot热图
colnames(data) <- c("Cancer",'Gene','Pearson','pvalue')
data$P[which(data$pvalue >0.05)] = '>0.05'
data$P[which(data$pvalue <0.05)] = '<0.05'
data$P=factor(data$P,ordered=T,levels=c('>0.05','<0.05'))
ggplot(data=data,aes(x=Gene,y=Cancer))+
geom_point(aes(size=P,fill=Pearson),shape=22,color="grey80")+
scale_fill_gradient2("Pearson' rho",low="#445393", high="#EE2627", mid="white")+
theme_bw()+
theme(panel.grid.major= element_blank(),
panel.grid.minor= element_blank(),
plot.title = element_text(hjust = 0.5, size = 12),
axis.text.y =element_text(size = 12, color = "black"),
axis.text.x.top=element_text(angle=90,hjust = 0,vjust = 0.1,
color = "black",size = 10),
axis.ticks = element_blank(),
legend.key.size = unit(0.15, "inches"))+
labs(x="",y=NULL)+
scale_size_discrete("p value",range=c(2,5))+
scale_x_discrete(position = "top")
计算坐标与角度
作图
ggplot() +
##热图1
geom_tile(data = data[which(data$group == 'treat'),],
aes(x = 1:nrow(data),y=1, height = 0.1,fill = logp),
color = 'white') +scale_fill_gradient2(midpoint = 2.97593,low="#445393", high="#EE2627", mid="white", name = 'P value', breaks <- c(0.1, 2.97593, 6.8),labels=c('NS', 'cutoff', 'S')) + new_scale("fill")+
##热图2
geom_tile(data = data[which(data$group == 'treat'),],
aes(x = 1:nrow(data), y=0.89, height = 0.1,fill = rho),
color = 'white') + scale_fill_viridis_c('Pearson’s rho', breaks = c(-0.33, 0, 0.33,0.68), labels = c(-0.33, 0, 0.33,0.68)) +
scale_y_continuous(expand = expansion(add = c(0.75,0.05)))+ ###中心扩圆
coord_polar(theta = 'x') +
# 添加基因注释1
new_scale("fill")+
geom_rect(data = name, aes(xmin = xmin,xmax=xmax,ymin = 1.17,ymax=1.27,fill =cancer)) +
scale_fill_manual(name = 'Cancer types',values = cb_palette) +
geom_text(data = name, ##标注行注释文本
aes(x = x,
y =1.3,
label = cancer, angle = ang, hjust = hjust), size = 3)+ guides(fill = "none")+
new_scale("fill")+
# 添加基因注释2
geom_rect(data = data,aes(xmin = xmin,xmax=xmax,ymin =1.06,ymax=1.16,fill= gene), color = NA) +
scale_fill_manual(name = 'Gene',
values = descolor1)+
new_scale("fill")+
theme_void()cancer=str_c("cancer",letters[1:5],sep=" ")
cancer=rep(cancer,8)
cancer=sort(cancer)
cancer=str_to_upper(cancer)
gene=rep(c("gene1","gene2","gene3","gene4"),10)
group=rep(c("treat","control"),each=4)
group=rep(group,5)
heat1=rnorm(40,0,1)
heat2=rnorm(40,10,5)
data=data.frame(cancer,gene,group,heat1,heat2)
#转换为长数据，且计算每层总格子数x
nrow=nrow(data)
x=
[1] 1 2 3 4 1 2 3 4 5 6 7 8 5 6 7 8 9 10 11 12 9 10 11 12 13 14 15 16 13 14 15 16 17 18 19 20 17
[38] 18 19 20
data$x=x
##计算角度，标记文本时用，所以新建一个angle。总的来说为总数/环数，计算坐标位点
res=data[which(data$group=="treat"),]
res$ang=seq(from=(360/nrow(res))/1.5,
to = (1.5* (360/nrow(res))) - 360,
length.out = nrow(res)) + 80
res$hjust <- 0
res$hjust[which(res$ang < -90)] <- 1
res$ang[which(res$ang < -90)] <- (180+res$ang)[which(res$ang < -90)]
res$x=seq(1:20)
res2=data[which(data$group=="control"),]
res2$ang=res$ang
res2$hjust=res$hjust
res2$x=seq(1:20)
data=rbind(res,res2)
##添加分环信息
data$group=factor(data$group)##factor个数对应环数,此处为treat和control两组
##作图
p1=ggplot(data,aes(x = x,y = group)) +
geom_tile(aes(fill = heat1),color = 'white') +
scale_fill_gradient2(midpoint = 0,
low = '#3C8DAD',
mid = "white",
high = '#FF6767') +
scale_y_discrete(expand = expansion(mult = c(2,0))) +
scale_x_discrete(expand = expansion(mult = c(0,0.05))) +
coord_polar(theta = 'x') + ##环形图
theme_void() +
geom_text(data = res, ##标注行注释文本
aes(x = x,
y = 4.6,
label = x, angle = ang, hjust = hjust), #x为id，可选择id的name
size = 2)
p1
##添加注释 添加第一个分组
annotation1=as.data.frame(res$cancer)
colnames(annotation1)="cancer"
###预设颜色
library(ggsci)
descolor1=pal_npg(palette = c("nrc"), alpha = 1)(10)
ggplot() +
geom_bar(data = annotation1,stat = 'identity', # 添加注释一
aes(x = 1:nrow(res),y = 0.25,fill = cancer),
width = 1,
color = NA) +
scale_fill_manual(name = 'annotation1',values = descolor1)
##再把热图加上
p=ggplot() +
geom_bar(data = annotation1,stat = 'identity', # 添加注释一
aes(x = 1:nrow(res),y = 0.25,fill = cancer), #y = 0.25 用来调整注释条与热图的相对位置
width = 1,
color = NA) +
scale_fill_manual(name = 'annotation1',values = descolor1)+
# 添加第一个环s1
# 新增图例
new_scale("fill") +
geom_tile(data = data[which(data$group == 'treat'),],
aes(x = 1:nrow(res),y = 1,fill = heat1),
color = 'white') +
scale_fill_gradient2(midpoint = 0,
low = 'green',
mid = "black",
high = 'red',
name = 'ONE') +
# 添加第一个环s2
geom_tile(data = data[which(data$group == 'control'),],
aes(x = 1:nrow(res),y = 2,fill = heat1),
color = 'white') +
ylim(-3,5) #ylim 参数，越负，环形热图中间就越空
p
library(circlize) ##rand_color函数
p + coord_polar(theta = 'x') +
theme_void() +
geom_text(data = res,
aes(x = x, ##x的id这一列，代表环形位置的
y = 4.6,
label = x, angle = ang, hjust = hjust),
# 给基因名添加颜色
color = rand_color(200),
size = 2)
4、添加多层注释
annotation1=as.data.frame(res$cancer)
colnames(annotation1)="cancer"
annotation2=as.data.frame(res$gene)
colnames(annotation2)="gene"
p1 <- ggplot() +
# 添加基因注释1
geom_bar(data = annotation1,stat = 'identity',
aes(x = 1:nrow(res),y = 0.25,fill = cancer),
width = 1,
color = NA) +
# 添加基因注释2
geom_bar(data = annotation2,stat = 'identity',
aes(x = 1:nrow(res),y = -0.25,fill = gene),
width = 1,
color = NA) +
scale_fill_manual(name = 'gene annotation',
values = descolor1)
p1
p2=p1+new_scale("fill") +
geom_tile(data = data[which(data$group == 'treat'),],
aes(x = 1:nrow(res),y = 1,fill = heat1),
color = 'white') +
scale_fill_gradient2(midpoint = 0,
low = 'green',
mid = "black",
high = 'red',
name = 'ONE') +
# 添加第一个环s2
geom_tile(data = data[which(data$group == 'control'),],
aes(x = 1:nrow(res),y = 2,fill = heat1),
color = 'white') +
ylim(-3,5)
p2
p3=p2 + coord_polar(theta = 'x') +
theme_void() + xlim(0,21) + ##xlim很重要，决定展示圆环的多少
geom_text(data = res,
aes(x = x,
y = 4.6,
label = x, angle = ang, hjust = hjust),
# 给基因名添加颜色
color = rand_color(20),
size = 2)
p3
有时候还需要对样本进行注释，同样的，添加条形图就完事
annotation1=as.data.frame(res$cancer)
colnames(annotation1)="cancer"
annotation2=as.data.frame(res$gene)
colnames(annotation2)="gene"
ringannotation1=as.data.frame(c("treat","control"))
colnames(ringannotation1)="group"
p3=p1+
new_scale("fill") +
geom_bar(data = ringannotation1,stat = 'identity',
aes(x = -2,y = 1,fill =factor(group)),
width = 5,
color = NA) +
scale_fill_manual(name = 'sample annotation',
values = c('control' = '#FA26A0','treat' = '#24A19C'))
p3
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