From thomas.baumann@ch.tum.de  Tue Feb 27 08:35:57 2001
From: thomas.baumann@ch.tum.de (Dr. Thomas Baumann)
Date: Tue, 27 Feb 2001 09:35:57 +0100 (CET)
Subject: [Rd] Patch to coplot.R
Message-ID: <200102270956.f1R9uGo26080@mafu.ws.chemie.tu-muenchen.de>

---1149173172-1804289383-983267779=:26068
Content-Type: TEXT/plain; charset=us-ascii

Hello,

and a big thank you for providing R!

Please find attached a diff for coplot which you may want to consider
for the next release. The diff is against R 1.2.2. The reasons for this
patch are:

1. The boxes of coplot did not align very well with the panel graphs if
   applied to a factor

2. Putting the levels as axis labels instead of just numbers makes the
   plot more readable

I also include a sample dataset (test.asc) and a sample program to show
the differences.

Thanks for looking at the code.

Thomas


---1149173172-1804289383-983267779=:26068
Content-Type: TEXT/plain; NAME="coplot.diff"

*** /tmp/mycoplot.R	Tue Feb 27 09:08:13 2001
--- /tmp/coplot.R.orig	Tue Feb 27 09:08:13 2001
***************
*** 201,227 ****
                  ...)
          }
          if ((i == total.rows) && (j%%2 == 0)) 
!             if (nlevels(x) > 0)
!               axis(1, labels = levels(x), xpd = NA)
!             else
!               axis(1, xpd = NA)
          else if ((i == istart || index + columns > nplots) && 
              (j%%2 == 1)) 
!             if (nlevels(x) > 0)
!               axis(3, labels = levels(x), xpd = NA)
!             else
!               axis(3, xpd = NA)
!         if ((j == 1) && ((total.rows - i)%%2 == 0))
!             if (nlevels(y) > 0)
!               axis(2, labels = levels(y), xpd = NA)
!             else
!               axis(2, xpd = NA)
          else if ((j == columns || index == nplots) && ((total.rows - 
!             i)%%2 == 1))
!             if (nlevels(y) > 0)
!               axis(4, labels = levels(y), xpd = NA)
!             else
!               axis(4, xpd = NA)
          box()
      }
      if (have.b) {
--- 201,215 ----
                  ...)
          }
          if ((i == total.rows) && (j%%2 == 0)) 
!             axis(1, xpd = NA)
          else if ((i == istart || index + columns > nplots) && 
              (j%%2 == 1)) 
!             axis(3, xpd = NA)
!         if ((j == 1) && ((total.rows - i)%%2 == 0)) 
!             axis(2, xpd = NA)
          else if ((j == columns || index == nplots) && ((total.rows - 
!             i)%%2 == 1)) 
!             axis(4, xpd = NA)
          box()
      }
      if (have.b) {
***************
*** 255,274 ****
          par(fig = c(0, f.col, f.row, 1), mar = nmar, new = TRUE)
          plot.new()
          nint <- nrow(a.intervals)
!         pwoffs <- nint / 32
!         plot.window(c(min(a.intervals[is.finite(a.intervals)] + pwoffs),
!                       max(a.intervals[is.finite(a.intervals)]) - pwoffs),
!                     0.5 + c(0, nint), log = "")
!         rect(a.intervals[, 1], 1:nint - 0.5, a.intervals[, 2], 
!             1:nint + 0.5, col = gray(0.95))
!         if (!is.null(a.levels)) {
              mid <- apply(a.intervals, 1, mean)
              text(mid, 1:nint, a.levels)
              NULL
          }
!         axis(3, labels = FALSE, tick = FALSE, xpd = NA)
!         axis(1, labels = FALSE, tick = FALSE)
!         box(col = "grey")
          mtext(xlab[2], side = 3, at = mean(par("usr")[1:2]), 
              line = 3, xpd = NA)
      }
--- 243,262 ----
          par(fig = c(0, f.col, f.row, 1), mar = nmar, new = TRUE)
          plot.new()
          nint <- nrow(a.intervals)
!         plot.window(range(a.intervals[is.finite(a.intervals)]), 
!             0.5 + c(0, nint), log = "")
!         bg <- if (is.null(a.levels)) 
!             gray(0.9)
!         else {
              mid <- apply(a.intervals, 1, mean)
              text(mid, 1:nint, a.levels)
              NULL
          }
!         rect(a.intervals[, 1], 1:nint - 0.3, a.intervals[, 2], 
!             1:nint + 0.3, col = bg)
!         axis(3, xpd = NA)
!         axis(1, labels = FALSE)
!         box()
          mtext(xlab[2], side = 3, at = mean(par("usr")[1:2]), 
              line = 3, xpd = NA)
      }
***************
*** 284,304 ****
              par(fig = c(f.col, 1, 0, f.row), mar = nmar, new = TRUE)
              plot.new()
              nint <- nrow(b.intervals)
!             pwoffs <- nint / 32
!             plot.window(0.5 + c(0, nint),
!                         c(min(b.intervals[is.finite(b.intervals)] + pwoffs),
!                           max(b.intervals[is.finite(b.intervals)]) - pwoffs),
!                         log = "")
!             rect(1:nint - 0.5, b.intervals[, 1], 1:nint + 0.5, 
!                 b.intervals[, 2], col = gray(0.95))
!             if (!is.null(b.levels)) {
                  mid <- apply(b.intervals, 1, mean)
                  text(1:nint, mid, b.levels, srt = 90)
                  NULL
              }
!             axis(4, labels = FALSE, tick = FALSE, xpd = NA)
!             axis(2, labels = FALSE, tick = FALSE)
!             box(col = "grey")
              mtext(ylab[2], side = 4, at = mean(par("usr")[3:4]), 
                  line = 3, xpd = NA)
          }
--- 272,291 ----
              par(fig = c(f.col, 1, 0, f.row), mar = nmar, new = TRUE)
              plot.new()
              nint <- nrow(b.intervals)
!             plot.window(0.5 + c(0, nint), range(b.intervals, 
!                 finite = TRUE), log = "")
!             bg <- if (is.null(b.levels)) 
!                 gray(0.9)
!             else {
                  mid <- apply(b.intervals, 1, mean)
                  text(1:nint, mid, b.levels, srt = 90)
                  NULL
              }
!             rect(1:nint - 0.3, b.intervals[, 1], 1:nint + 0.3, 
!                 b.intervals[, 2], col = bg)
!             axis(4, xpd = NA)
!             axis(2, labels = FALSE)
!             box()
              mtext(ylab[2], side = 4, at = mean(par("usr")[3:4]), 
                  line = 3, xpd = NA)
          }

---1149173172-1804289383-983267779=:26068
Content-Type: TEXT/plain; NAME="mycoplot.R"

function (formula, data, given.values, panel = points, rows, 
    columns, show.given = TRUE, col = par("fg"), pch = par("pch"), 
    xlab = c(x.name, paste("Given :", a.name)), ylab = c(y.name, 
        paste("Given :", b.name)), subscripts = FALSE, number = 6, 
    overlap = 0.5, xlim, ylim, ...) 
{
    deparen <- function(expr) {
        while (is.language(expr) && !is.name(expr) && deparse(expr[[1]]) == 
            "(") expr <- expr[[2]]
        expr
    }
    bad.formula <- function() stop("invalid conditioning formula")
    bad.lengths <- function() stop("incompatible variable lengths")
    formula <- deparen(formula)
    if (!inherits(formula, "formula")) 
        bad.formula()
    y <- deparen(formula[[2]])
    rhs <- deparen(formula[[3]])
    if (deparse(rhs[[1]]) != "|") 
        bad.formula()
    x <- deparen(rhs[[2]])
    rhs <- deparen(rhs[[3]])
    if (is.language(rhs) && !is.name(rhs) && (deparse(rhs[[1]]) == 
        "*" || deparse(rhs[[1]]) == "+")) {
        have.b <- TRUE
        a <- deparen(rhs[[2]])
        b <- deparen(rhs[[3]])
    }
    else {
        have.b <- FALSE
        a <- rhs
    }
    if (missing(data)) 
        data <- parent.frame()
    x.name <- deparse(x)
    x <- eval(x, data, parent.frame())
    nobs <- length(x)
    y.name <- deparse(y)
    y <- eval(y, data, parent.frame())
    if (length(y) != nobs) 
        bad.lengths()
    a.name <- deparse(a)
    a <- eval(a, data, parent.frame())
    if (length(a) != nobs) 
        bad.lengths()
    if (is.character(a)) 
        a <- as.factor(a)
    a.levels <- NULL
    if (have.b) {
        b.levels <- NULL
        b.name <- deparse(b)
        b <- eval(b, data, parent.frame())
        if (length(b) != nobs) 
            bad.lengths()
        if (is.character(b)) 
            b <- as.factor(b)
        missingrows <- which(is.na(x) | is.na(y) | is.na(a) | 
            is.na(b))
    }
    else {
        missingrows <- which(is.na(x) | is.na(y) | is.na(a))
        b <- NULL
        b.name <- ""
    }
    number <- as.integer(number)
    if (length(number) == 0 || any(number < 1)) 
        stop("number must be integer >= 1")
    if (any(overlap >= 1)) 
        stop("overlap must be < 1 (and typically >= 0).")
    bad.givens <- function() stop("invalid given.values")
    if (missing(given.values)) {
        a.intervals <- if (is.factor(a)) {
            i <- 1:nlevels(a)
            a.levels <- levels(a)
            a <- as.numeric(a)
            cbind(i - 0.5, i + 0.5)
        }
        else co.intervals(a, number = number[1], overlap = overlap[1])
        b.intervals <- if (have.b) {
            if (is.factor(b)) {
                i <- 1:nlevels(b)
                b.levels <- levels(b)
                b <- as.numeric(b)
                cbind(i - 0.5, i + 0.5)
            }
            else {
                if (length(number) == 1) 
                  number <- rep(number, 2)
                if (length(overlap) == 1) 
                  overlap <- rep(overlap, 2)
                co.intervals(b, number = number[2], overlap = overlap[2])
            }
        }
    }
    else {
        if (!is.list(given.values)) 
            given.values <- list(given.values)
        if (length(given.values) != (if (have.b) 
            2
        else 1)) 
            bad.givens()
        a.intervals <- given.values[[1]]
        if (is.factor(a)) {
            if (is.character(a.intervals)) 
                a.intervals <- match(a.intervals, levels(a))
            a.intervals <- cbind(a.intervals - 0.5, a.intervals + 
                0.5)
            a.levels <- levels(a)
            a <- as.numeric(a)
        }
        else if (is.numeric(a)) {
            if (!is.numeric(a.intervals)) 
                bad.givens()
            if (!is.matrix(a.intervals) || ncol(a.intervals) != 
                2) 
                a.intervals <- cbind(a.intervals - 0.5, a.intervals + 
                  0.5)
        }
        if (have.b) {
            b.intervals <- given.values[[2]]
            if (is.factor(b)) {
                if (is.character(b.intervals)) 
                  b.intervals <- match(b.intervals, levels(b))
                b.intervals <- cbind(b.intervals - 0.5, b.intervals + 
                  0.5)
                b.levels <- levels(b)
                b <- as.numeric(b)
            }
            else if (is.numeric(b)) {
                if (!is.numeric(b.intervals)) 
                  bad.givens()
                if (!is.matrix(b.intervals) || ncol(b.intervals) != 
                  2) 
                  b.intervals <- cbind(b.intervals - 0.5, b.intervals + 
                    0.5)
            }
        }
    }
    if (any(is.na(a.intervals)) || (have.b && any(is.na(b.intervals)))) 
        bad.givens()
    if (have.b) {
        rows <- nrow(b.intervals)
        columns <- nrow(a.intervals)
        nplots <- rows * columns
        if (length(show.given) < 2) 
            show.given <- rep(show.given, 2)
    }
    else {
        nplots <- nrow(a.intervals)
        if (missing(rows)) {
            if (missing(columns)) {
                rows <- ceiling(round(sqrt(nplots)))
                columns <- ceiling(nplots/rows)
            }
            else rows <- ceiling(nplots/columns)
        }
        else if (missing(columns)) 
            columns <- ceiling(nplots/rows)
        if (rows * columns < nplots) 
            stop("rows * columns too small")
    }
    total.columns <- columns
    total.rows <- rows
    f.col <- f.row <- 1
    if (show.given[1]) {
        total.rows <- rows + 1
        f.row <- rows/total.rows
    }
    if (have.b && show.given[2]) {
        total.columns <- columns + 1
        f.col <- columns/total.columns
    }
    opar <- par(mfrow = c(total.rows, total.columns), oma = if (have.b) 
        rep(5, 4)
    else c(5, 6, 5, 4), mar = if (have.b) 
        rep(0, 4)
    else c(0.5, 0, 0.5, 0), new = FALSE)
    on.exit(par(opar))
    plot.new()
    if (missing(xlim)) 
        xlim <- range(x[is.finite(x)])
    if (missing(ylim)) 
        ylim <- range(y[is.finite(y)])
    pch <- rep(pch, length = nobs)
    col <- rep(col, length = nobs)
    do.panel <- function(index, subscripts = FALSE) {
        istart <- (total.rows - rows) + 1
        i <- total.rows - ((index - 1)%/%columns)
        j <- (index - 1)%%columns + 1
        par(mfg = c(i, j, total.rows, total.columns))
        plot.new()
        plot.window(xlim, ylim, log = "")
        if (any(is.na(id))) 
            id[is.na(id)] <- FALSE
        if (any(id)) {
            grid(lty = "solid")
            if (subscripts) 
                panel(x[id], y[id], subscripts = id, col = col[id], 
                  pch = pch[id], ...)
            else panel(x[id], y[id], col = col[id], pch = pch[id], 
                ...)
        }
        if ((i == total.rows) && (j%%2 == 0)) 
            if (nlevels(x) > 0)
              axis(1, labels = levels(x), xpd = NA)
            else
              axis(1, xpd = NA)
        else if ((i == istart || index + columns > nplots) && 
            (j%%2 == 1)) 
            if (nlevels(x) > 0)
              axis(3, labels = levels(x), xpd = NA)
            else
              axis(3, xpd = NA)
        if ((j == 1) && ((total.rows - i)%%2 == 0))
            if (nlevels(y) > 0)
              axis(2, labels = levels(y), xpd = NA)
            else
              axis(2, xpd = NA)
        else if ((j == columns || index == nplots) && ((total.rows - 
            i)%%2 == 1))
            if (nlevels(y) > 0)
              axis(4, labels = levels(y), xpd = NA)
            else
              axis(4, xpd = NA)
        box()
    }
    if (have.b) {
        count <- 1
        for (i in 1:rows) {
            for (j in 1:columns) {
                id <- ((a.intervals[j, 1] <= a) & (a <= a.intervals[j, 
                  2]) & (b.intervals[i, 1] <= b) & (b <= b.intervals[i, 
                  2]))
                do.panel(count, subscripts)
                count <- count + 1
            }
        }
    }
    else {
        for (i in 1:nplots) {
            id <- ((a.intervals[i, 1] <= a) & (a <= a.intervals[i, 
                2]))
            do.panel(i, subscripts)
        }
    }
    mtext(xlab[1], side = 1, at = 0.5 * f.col, outer = TRUE, 
        line = 3.5, xpd = NA)
    mtext(ylab[1], side = 2, at = 0.5 * f.row, outer = TRUE, 
        line = 3.5, xpd = NA)
    if (length(xlab) == 1) 
        xlab <- c(xlab, paste("Given :", a.name))
    if (show.given[1]) {
        mar <- par("mar")
        nmar <- mar + c(4, 0, 0, 0)
        par(fig = c(0, f.col, f.row, 1), mar = nmar, new = TRUE)
        plot.new()
        nint <- nrow(a.intervals)
        pwoffs <- nint / 32
        plot.window(c(min(a.intervals[is.finite(a.intervals)] + pwoffs),
                      max(a.intervals[is.finite(a.intervals)]) - pwoffs),
                    0.5 + c(0, nint), log = "")
        rect(a.intervals[, 1], 1:nint - 0.5, a.intervals[, 2], 
            1:nint + 0.5, col = gray(0.95))
        if (!is.null(a.levels)) {
            mid <- apply(a.intervals, 1, mean)
            text(mid, 1:nint, a.levels)
            NULL
        }
        axis(3, labels = FALSE, tick = FALSE, xpd = NA)
        axis(1, labels = FALSE, tick = FALSE)
        box(col = "grey")
        mtext(xlab[2], side = 3, at = mean(par("usr")[1:2]), 
            line = 3, xpd = NA)
    }
    else {
        mtext(xlab[2], side = 3, at = 0.5 * f.col, line = 3.25, 
            outer = TRUE, xpd = NA)
    }
    if (have.b) {
        if (length(ylab) == 1) 
            ylab <- c(ylab, paste("Given :", b.name))
        if (show.given[2]) {
            nmar <- mar + c(0, 4, 0, 0)
            par(fig = c(f.col, 1, 0, f.row), mar = nmar, new = TRUE)
            plot.new()
            nint <- nrow(b.intervals)
            pwoffs <- nint / 32
            plot.window(0.5 + c(0, nint),
                        c(min(b.intervals[is.finite(b.intervals)] + pwoffs),
                          max(b.intervals[is.finite(b.intervals)]) - pwoffs),
                        log = "")
            rect(1:nint - 0.5, b.intervals[, 1], 1:nint + 0.5, 
                b.intervals[, 2], col = gray(0.95))
            if (!is.null(b.levels)) {
                mid <- apply(b.intervals, 1, mean)
                text(1:nint, mid, b.levels, srt = 90)
                NULL
            }
            axis(4, labels = FALSE, tick = FALSE, xpd = NA)
            axis(2, labels = FALSE, tick = FALSE)
            box(col = "grey")
            mtext(ylab[2], side = 4, at = mean(par("usr")[3:4]), 
                line = 3, xpd = NA)
        }
        else {
            mtext(ylab[2], side = 4, at = 0.5 * f.row, line = 3.25, 
                outer = TRUE, xpd = NA)
        }
    }
    if (length(missingrows) > 0) {
        cat("\nMissing rows:", missingrows, "\n")
        invisible(missingrows)
    }
}

---1149173172-1804289383-983267779=:26068
Content-Type: TEXT/plain; NAME="test.asc"

RDA1
5 0
9 row.names
5 names
5 class
6 levels
3 cxt
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2 0 0
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 0.9629377
 0.96566601
 0.9679529100000001
 0.9834591
-1

2 0 0
1 0 0
3
-1
16 0 0
1
 10 data.frame
-1
2 0 0
1 0 0
2
-1
16 0 0
4
 6 loc.id
 7 chem.id
 4 mode
 6 fitpar
-1
2 0 0
1 0 0
1
-1
16 0 0
90
 1 1
 1 2
 1 3
 1 4
 1 5
 1 6
 1 7
 1 8
 1 9
 2 10
 2 11
 2 12
 2 13
 2 14
 2 15
 2 16
 2 17
 2 18
 2 19
 2 20
 2 21
 2 22
 2 23
 2 24
 2 25
 2 26
 2 27
 2 28
 2 29
 2 30
 2 31
 2 32
 2 33
 2 34
 2 35
 2 36
 2 37
 2 38
 2 39
 2 40
 2 41
 2 42
 2 43
 2 44
 2 45
 2 46
 2 47
 2 48
 2 49
 2 50
 2 51
 2 52
 2 53
 2 54
 2 55
 2 56
 2 57
 2 58
 2 59
 2 60
 2 61
 2 62
 2 63
 2 64
 2 65
 2 66
 2 67
 2 68
 2 69
 2 70
 2 71
 2 72
 2 73
 2 74
 2 75
 2 76
 2 77
 2 78
 2 79
 2 80
 2 81
 2 82
 2 83
 2 84
 2 85
 2 86
 2 87
 2 88
 2 89
 2 90
-1
-1
-1
-1
-1
-1
-1

---1149173172-1804289383-983267779=:26068
Content-Type: TEXT/plain; NAME="coplot_sample.R"

load("test.asc")
mycoplot(cxt$fitpar ~ unclass(cxt$loc.id)|
         cxt$chem.id * cxt$mode,
         panel = points,
         bg = "blue",
         col = "blue",
         pch = 21,
         xlab = c("Location", "Contaminant"),
         ylab = c(label, "CXTFit-Mode"),
         ylim = c(0.6,1)
       )


coplot(cxt$fitpar ~ unclass(cxt$loc.id)|
         cxt$chem.id * cxt$mode,
         panel = points,
         bg = "blue",
         col = "blue",
         pch = 21,
         xlab = c("Location", "Contaminant"),
         ylab = c(label, "CXTFit-Mode"),
         ylim = c(0.6,1)
       )

---1149173172-1804289383-983267779=:26068--
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[Rd] Patch to coplot.R
Dr. Thomas Baumann