4 Figure3

4.1 Fig.3a

df = read.csv('data/3A.csv',header = T,row.names = 1)
head(df[1:3,1:3])

##            chr1       chr2       chr3
## chr1 0.00000000 0.03254124 0.04552237
## chr2 0.03254124 0.00000000 0.03214177
## chr3 0.04552237 0.03214177 0.00000000

library(RColorBrewer)
suppressMessages(library(pheatmap))
pheatmap(df,
         color = rev(colorRampPalette(c(brewer.pal(9,"Spectral")))(100))
         )

4.2 Fig.3b

df = read.table('data/3b_data',header = T)
head(df)[1:3,1:3]

##   V103 V102 V101
## 1    0    0    0
## 2    0    0    0
## 3    0    0    0

df = as.matrix(df)
suppressMessages(library(matlab))
suppressMessages(library(fields))
library(RColorBrewer)
col.ls <- colorRampPalette(c('red','white'))(4000)
col.ls <- rev(col.ls)
image.plot(x = 1:nrow(df), y = 1:ncol(df), z = df,  xlab = "", ylab = "", col = col.ls, cex = 1, axes=F,legend.cex = 0)
box()

4.3 Fig.3c

df = read.table('data/3c_data',header = T)
head(df)

##   Group      value
## 1 chr13 0.03869764
## 2 chr13 0.03388018
## 3 chr13 0.04395268
## 4 chr13 0.03348364
## 5 chr13 0.05039276
## 6 chr13 0.05006650

df$Group = factor(df$Group,levels = c('chr13','14','15','21','22'))
boxplot(df$value ~ df$Group ,
        col = c(rep('skyblue',2),rep('orange',3)),
        ylab = 'Normalized contacts',
        las = 1,xlab = '',outline=F,ylim = c(0,0.12))

4.4 Fig.3d

df = read.table('data/3d_data',header = T)
head(df)

##   Group      value
## 1 chr13 0.04986233
## 2 chr13 0.06765239
## 3 chr13 0.08644709
## 4 chr13 0.06756526
## 5    14 0.04986233
## 6    14 0.07438547

df$Group = factor(df$Group,levels = c('chr13','14','15','21','22'))
boxplot(df$value ~ df$Group ,
        col = c(rep('skyblue',2),rep('orange',3)),
        ylab = 'Normalized contacts',
        las = 1,xlab = '',outline=F,ylim = c(0,0.15))

4.5 Fig.3f

data <- data.frame(
  group=c('rDNA-rDNA','rDNA-Other'),
  value=c(76,24)
)
suppressMessages(library(ggplot2))
suppressMessages(library(dplyr))
data <- data %>% 
  arrange(desc(group)) %>%
  mutate(prop = value / sum(data$value) *100) %>%
  mutate(ypos = cumsum(prop)- 0.5*prop )
ggplot(data, aes(x="", y=prop, fill=group)) +
  geom_bar(stat="identity", width=1, color="white") +
  coord_polar("y", start=0) +
  theme_void() + 
  theme(legend.position="none") +
  geom_text(aes(y = ypos, label = group), color = "white", size=6) +
  scale_fill_manual(values = c('#5A94CF','#A0CC58'))

4.6 Fig.3h

df = read.table('data/3h_data',header = T)
head(df)

##   chrom       num group
## 1  chr1  9.780517   hic
## 2 chr10  8.399322   hic
## 3 chr11  7.512230   hic
## 4 chr12 10.223240   hic
## 5 chr13  6.110973   hic
## 6 chr14 12.422969   hic

df$chrom = factor(df$chrom,paste0('chr',c(1:22,'X')))
suppressMessages(library(ggpubr))
ggplot(df, aes(x=chrom, y=num, fill=group)) + 
  geom_bar(stat="identity", width=0.7, position=position_dodge(width=0.8))+
  theme_pubr()+scale_fill_manual(values=c("#42B256","#CC5C55"))+
  ylab('Normalized interactions with rDNA')+xlab('')