update lect11

lect11-epigenetics/Makefile

@@ -0,0 +1,12 @@
+RMD := $(wildcard *.rmd) $(wildcard *.Rmd)
+PDF := $(RMD:.rmd=-slides.pdf) $(RMD:.Rmd=-beamer.pdf)
+HTML := $(RMD:.rmd=.html) $(RMD:.Rmd=.html)
+TEX := $(RMD:.rmd=.tex) $(RMD:.Rmd=.tex)
+
+all: $(PDF)
+
+clean:
+	rm -f $(PDF)
+
+%-beamer.pdf: %.Rmd
+	Rscript -e "rmarkdown::render('$<', output_format='beamer_presentation', output_file='$@');"

lect11-epigenetics/Setup.R

@@ -0,0 +1,210 @@
+options(stringsAsFactors = FALSE)
+
+`%&%` <- function(a,b) paste0(a, b)
+`%r%` <- function(mat,rr) mat[rr, , drop = FALSE]
+`%c%` <- function(mat,cc) mat[, cc, drop = FALSE]
+
+library(tidyverse)
+library(data.table)
+library(ggrepel)
+
+num.int <- function(...) format(..., justify="none", big.mark=",", drop0trailing = TRUE)
+
+num.sci <- function(...) format(..., justify="none", digits=2, scientific = TRUE)
+
+row.order <- function(mat) {
+    require(cba)
+    require(proxy)
+
+    if(nrow(mat) < 3) {
+        return(1:nrow(mat))
+    }
+
+    D = proxy::dist(mat, method <- function(a,b) 1 - cor(a,b, method = 'spearman'))
+    D[!is.finite(D)] = 0
+    h.out = hclust(D)
+    o.out = cba::order.optimal(D, h.out$merge)
+    return(o.out$order)
+}
+
+col.order <- function(pair.tab, .ro, ret.tab = FALSE) {
+
+    M = pair.tab %>%
+        dplyr::select(row, col, weight) %>%
+        dplyr::mutate(row = factor(row, .ro)) %>%
+        tidyr::spread(key = col, value = weight, fill = 0)
+
+    co = order(apply(M[, -1], 2, which.max), decreasing = TRUE)
+    .co = colnames(M)[-1][co]
+    if(ret.tab) {
+        ret = pair.tab %>%
+            dplyr::mutate(row = factor(row, .ro)) %>%
+            dplyr::mutate(col = factor(col, .co))
+    } else {
+        ret = .co
+    }
+    return(ret)
+}
+
+order.pair <- function(pair.tab, ret.tab=FALSE) {
+
+    require(tidyr)
+    require(dplyr)
+
+    .tab = pair.tab %>% dplyr::select(row, col, weight)
+
+    M = .tab %>% tidyr::spread(key = col, value = weight, fill = 0)
+    rr = M[, 1] %>% unlist(use.names = FALSE)
+    cc = colnames(M)[-1] %>% unlist(use.names = FALSE)
+
+    ## log.msg('Built the Mat: %d x %d', nrow(M), ncol(M))
+    ro = row.order(M %>% dplyr::select(-row) %>% as.matrix())
+
+    ## log.msg('Sort the rows: %d', length(ro))
+    co = order(apply(M[ro, -1], 2, which.max), decreasing = TRUE)
+
+    ## co = row.order(t(M %>% dplyr::select(-row) %>% as.matrix()))
+    ## log.msg('Sort the columns: %d', length(co))
+
+    if(ret.tab){
+        ret = pair.tab %>%
+            dplyr::mutate(row = factor(row, rr[ro])) %>%
+            dplyr::mutate(col = factor(col, cc[co]))
+    } else {
+        ret = list(rows = rr[ro], cols = cc[co], M = M)
+    }
+
+    return(ret)
+}
+
+
+.sort.matrix <- function(.X) {
+    as.matrix(.X) %>%
+        reshape2::melt() %>%
+        rename(row = Var1, col = Var2, weight = value) %>%
+        order.pair(ret.tab=TRUE) %>%
+        as.data.table %>%
+        dcast(row ~ col, value.var = "weight") %>%
+        dplyr::select(-row) %>%
+        as.matrix
+}
+
+.rnorm <- function(d1, d2) {
+    matrix(rnorm(d1 * d2), d1, d2)
+}
+
+###############################################################
+.matshow <- function(.mat, .lab = 1, .axis.lab=8, .lw = .1, .scale=TRUE) {
+
+    .mat <- as.matrix(.mat)
+    .cols <- colnames(.mat)
+    .rows <- rownames(.mat)
+    if(length(.cols) < ncol(.mat)){
+        colnames(.mat) <- str_c("c", 1:ncol(.mat))
+    }
+    if(length(.rows) < nrow(.mat)){
+        rownames(.mat) <- str_c("r", 1:nrow(.mat))
+    }
+    .cols <- colnames(.mat)
+    .rows <- rownames(.mat)
+
+    .dt <-
+        as.data.frame(.mat) %>%
+        rownames_to_column("row") %>% 
+        as.data.table %>%
+        melt(id.vars = "row", variable.name = "col") %>%
+        dplyr::mutate(row = factor(as.character(row), rev(.rows))) %>%
+        dplyr::mutate(col = factor(as.character(col), .cols))
+
+    ret <-
+        ggplot(.dt, aes(y = row, x = col, fill = value)) +
+        theme(legend.position = "none") +
+        theme(axis.text.x = element_text(size=.axis.lab, angle=90, vjust=1, hjust=1)) +
+        theme(axis.text.y = element_text(size=.axis.lab)) +
+        theme(axis.title = element_blank()) +
+        geom_tile(linewidth = .lw, colour = "black")
+
+    if(.scale){
+        ret <- ret +
+            scale_fill_distiller(palette = "RdBu", direction = -1)
+    } else {
+        ret <- ret +
+            scale_fill_distiller(palette = "Greys", direction = 1)
+    }
+
+    if(.lab > 0) {
+        ret <- ret +
+            geom_text(aes(label = round(value,1)), size = .lab)
+    }
+
+    return(ret)
+}
+
+################################################################
+.gg.plot <- function(...) {
+    ggplot(...) +
+        theme_classic() +
+        theme(axis.title = element_text(size=8)) +
+        theme(axis.text = element_text(size=6)) +
+        theme(legend.spacing = unit(.1, "lines"),
+              legend.key.size = unit(.5, "lines"),
+              legend.text = element_text(size=5),
+              legend.title = element_text(size=6),
+              panel.background = element_rect(fill='transparent'),
+              plot.background = element_rect(fill='transparent', color=NA),
+              legend.background = element_rect(fill='transparent', size=0.05),
+              legend.box.background = element_rect(fill='transparent'))
+}
+
+as.dt <- function(x, col.names=NULL) {
+    .mat <- as.matrix(x)
+    if(is.null(col.names)) col.names <- str_c("V",1:ncol(.mat))
+    colnames(.mat) <- col.names
+    as.data.table(.mat)
+}
+
+################################################################
+if.needed <- function(.file, .code) {
+    if(!all(file.exists(unlist(.file)))){ .code }
+    stopifnot(all(file.exists(unlist(.file))))
+}
+
+################################################################
+setup.env <- function(fig.dir) {
+
+    ## save figures here
+    dir.create(fig.dir, showWarnings = FALSE, recursive = TRUE)
+    knitr::opts_chunk$set(warning = FALSE, message = FALSE, fig.path = fig.dir)
+    knitr::opts_chunk$set(echo=FALSE, fig.align="center")
+
+    ## allow the code to chunk set size="tiny" ##
+    hook.chunk  <- knitr::knit_hooks$get("chunk")
+
+    ## Default: normalsize -> scriptsize
+    ## This will redefine normalsize
+    knitr::knit_hooks$set(chunk = function(x, options) {
+        x <- hook.chunk(x, options)
+        ifelse(options$size != "normalsize",
+               paste0("\n \\", options$size, "\n\n", x, "\n\n \\normalsize"),
+               paste0("\n \\", "scriptsize", "\n\n", x, "\n\n \\normalsize"))
+    })
+
+    ## show plot one by one in beamer ##
+    hook.plot <- knitr::knit_hooks$get("plot")
+
+    knitr::knit_hooks$set(plot = function(x, options) {
+        if (!is.null(options$onslide.plot)) {
+            bf <- paste0("\\onslide<", options$onslide.plot, ">{")
+            ret <- paste(c(bf, knitr::hook_plot_tex(x, options), "}"),
+                         collapse = "\n")
+            return(ret)
+        } else if (!is.null(options$only.plot)) {
+            bf <- paste0("\\only<", options$only.plot, ">{")
+            ret <- paste(c(bf, knitr::hook_plot_tex(x, options), "}"),
+                         collapse = "\n")
+            return(ret)
+        }
+        return(hook.plot(x, options))
+    })
+}
+