Chapter 7 diffBD chromatin state across cells

7.1 Description

• explore the chromatin states dynamics arcross cells per CBS sets
• chromHMM files are download from Roadmap project

7.2 Load chromHMM files

## Section: load data
##################################################
file.ls <- list.files('data/chromHMM-Roadmap/', pattern = 'Mid', full = T)
file.ls <- file.ls[c(5,2,3,1)]

7.3 Get the chromatin state dynamics

sample.ls <- c('Stable', 'Hepatocyte', 'Myocyte', 'Bcell')

mat.ls <- 1:4 %>% map( ~ {
  f <- file.ls[.x]
  sample <- sample.ls[.x]
  
  mat <- fread(f)
  mat <- mat[, c(4, 5, 9)]
  mat <- dcast(mat, V4 ~ V5)
  colnames(mat)[1] <- 'id'
  
  mat <-
    mgsub::mgsub(
      mat,
      c(
        "1_TssA",
        "2_TssAFlnk",
        "3_TxFlnk",
        "4_Tx",
        "5_TxWk",
        "6_EnhG",
        "7_Enh",
        "8_ZNF/Rpts",
        "9_Het",
        "10_TssBiv",
        "11_BivFlnk",
        "12_EnhBiv",
        "13_ReprPC",
        "14_ReprPCWk",
        "15_Quies"
      ),
      seq(1, 15)
    )
  mat$E007 <- as.numeric(mat$E007)
  mat$E032 <- as.numeric(mat$E032)
  mat$E066 <- as.numeric(mat$E066)
  mat$E121 <- as.numeric(mat$E121)
  
  return(mat)
  
  
})

## Using 'V9' as value column. Use 'value.var' to override
## Using 'V9' as value column. Use 'value.var' to override
## Using 'V9' as value column. Use 'value.var' to override
## Using 'V9' as value column. Use 'value.var' to override

7.4 Heatmap showing the dynamics

myColor <-
  c(
    rgb(255, 0, 0, maxColorValue = 255),
    rgb(255, 69, 0, maxColorValue = 255),
    rgb(50, 205, 50, maxColorValue = 255),
    rgb(0, 128, 0, maxColorValue = 255),
    rgb(0, 100, 0, maxColorValue = 255),
    rgb(194, 225, 5, maxColorValue = 255),
    rgb(255, 255, 0, maxColorValue = 255),
    rgb(102, 205, 170, maxColorValue = 255),
    rgb(138, 145, 208, maxColorValue = 255),
    rgb(205, 92, 92, maxColorValue = 255),
    rgb(233, 150, 122, maxColorValue = 255),
    rgb(189, 183, 107, maxColorValue = 255),
    rgb(128, 128, 128, maxColorValue = 255),
    rgb(192, 192, 192, maxColorValue = 255),
    rgb(230, 230, 230, maxColorValue = 255)
  )
myBreaks <- seq(0, 15, 1)

map2(mat.ls, sample.ls, ~ {
  pp <-
    pheatmap(
      .x[, c(4, 5, 3)],
      color = myColor,
      breaks = myBreaks,
      show_rownames = F,
      cluster_cols = F,
      main = .y
    )
  pp
})

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