4C

single_Vplot = function(input){
v <- read_vplot(input)

v$label = c(nrow(v):1)
v = v[order(v$label),-ncol(v)]

data = v

options(repr.plot.width = 2.5, repr.plot.height = 3, repr.plot.res = 1500, repr.plot.pointsize = 10)
conte=data
namen = c(1:nrow(data))
rownames(conte)=as.vector(namen)
PCA=conte
vvv=pheatmap(PCA,
         cluster_rows = F,
         cluster_cols = F,
         show_rownames = F,
         show_colnames = F,
         legend = FALSE,
         border_color = FALSE,
         color = colorRampPalette(c("white","dodgerblue1","dodgerblue2","dodgerblue3","dodgerblue4","darkblue"))(100),
         breaks=seq(from=0,to=2,length.out = 100))
vvv
    }

diff_Vplot = function(DAY0,DAY4){
DAY0 <- read_vplot(DAY0)
DAY4 <- read_vplot(DAY4)

v = DAY4 - DAY0 
v$label = c(nrow(v):1)
v = v[order(v$label),-ncol(v)]

data = v

options(repr.plot.width = 2.5, repr.plot.height = 3, repr.plot.res = 1500, repr.plot.pointsize = 10)
conte=data
namen = c(1:nrow(data))
rownames(conte)=as.vector(namen)
PCA=conte
vvv=pheatmap(PCA,
         cluster_rows = F,
         cluster_cols = F,
         show_rownames = F,
         show_colnames = F,
         legend = FALSE,
         border_color = FALSE,
         color = colorRampPalette(c("darkblue","blue","skyblue","pink","red","darkred"))(100),
         breaks=seq(from=-1,to=1,length.out = 100))
vvv
    }

# LINUX cmd

# pyatac vplot \
# --bam /data3/psg/Ets1/DAY0_ATAC.bam \
# --bed /data3/psg/Ets1/DAY0_NOR_Ets1.txt \
# --out /data3/psg/Ets1/DAY0_NOR_Ets1_50_800_300_10_5_V --cores 7 --lower 50 --upper 800 --flank 300 --weight 10 --strand 5 --scale

# pyatac vplot \
# --bam /data3/psg/Ets1/DAY4_ATAC.bam \
# --bed /data3/psg/Ets1/DAY4_NOR_Ets1.txt \
# --out /data3/psg/Ets1/DAY4_NOR_Ets1_50_800_300_10_5_V --cores 7 --lower 50 --upper 800 --flank 300 --weight 10 --strand 5 --scale

single_Vplot(input="/data3/psg/Ets1/DAY0_NOR_Ets1_50_800_300_10_5_V.Mat")

Image

single_Vplot(input="/data3/psg/Ets1/DAY4_NOR_Ets1_50_800_300_10_5_V.Mat")

Image

diff_Vplot(DAY0 = "/data3/psg/Ets1/DAY0_NOR_Ets1_50_800_300_10_5_V.Mat",
           DAY4 = "/data3/psg/Ets1/DAY4_NOR_Ets1_50_800_300_10_5_V.Mat")

Image