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# Adapted originally from the very excellent pheatmap package
# (https://cran.r-project.org/web/packages/pheatmap/index.html)
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#' @importFrom gtable gtable
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.lo <- function(rown,
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coln,
nrow,
ncol,
cellHeight = NA,
cellWidth = NA,
treeHeightCol,
treeHeightRow,
legend,
annotationRow,
annotationCol,
annotationColors,
annotationLegend,
annotationNamesRow,
annotationNamesCol,
main,
fontSize,
fontSizeRow,
fontSizeCol,
gapsRow,
gapsCol,
...) {
# Get height of colnames and length of rownames
if (!is.null(coln[1]) |
(!.is.na2(annotationRow) & annotationNamesRow)) {
if (!is.null(coln[1])) {
t <- coln
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} else {
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t <- ""
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}
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tw <- strwidth(t, units = "in", cex = fontSizeCol / fontSize)
if (annotationNamesRow) {
t <- c(t, colnames(annotationRow))
tw <- c(tw, strwidth(colnames(annotationRow), units = "in"))
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}
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longestColn <- which.max(tw)
gp <- list(fontSize = ifelse(longestColn <= length(coln),
fontSizeCol,
fontSize
), ...)
colnHeight <- unit(
1,
"grobheight",
textGrob(t[longestColn],
rot = 90,
gp = do.call(gpar, gp)
)
) +
unit(10, "bigpts")
} else {
colnHeight <- unit(5, "bigpts")
}
if (!is.null(rown[1])) {
t <- rown
tw <- strwidth(t, units = "in", cex = fontSizeRow / fontSize)
if (annotationNamesCol) {
t <- c(t, colnames(annotationCol))
tw <- c(tw, strwidth(colnames(annotationCol), units = "in"))
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}
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longestRown <- which.max(tw)
gp <- list(fontSize = ifelse(longestRown <= length(rown),
fontSizeRow,
fontSize
), ...)
rownWidth <- unit(
1,
"grobwidth",
textGrob(t[longestRown],
gp = do.call(gpar, gp)
)
) +
unit(10, "bigpts")
} else {
rownWidth <- unit(5, "bigpts")
}
gp <- list(fontSize = fontSize, ...)
# Legend position
if (!.is.na2(legend)) {
longestBreak <- which.max(nchar(names(legend)))
longestBreak <- unit(
1.1,
"grobwidth",
textGrob(as.character(names(legend))[longestBreak],
gp = do.call(gpar, gp)
)
)
titleLength <- unit(
1.1,
"grobwidth",
textGrob("Scale",
gp = gpar(
fontface = "bold",
...
)
)
)
legendWidth <- unit(12, "bigpts") + longestBreak * 1.2
legendWidth <- max(titleLength, legendWidth)
} else {
legendWidth <- unit(0, "bigpts")
}
# Set main title height
if (is.na(main)) {
mainHeight <- unit(0, "npc")
} else {
mainHeight <- unit(
1.5,
"grobheight",
textGrob(main,
gp = gpar(
fontSize = 1.3 * fontSize,
...
)
)
)
}
# Column annotations
textheight <- unit(fontSize, "bigpts")
if (!.is.na2(annotationCol)) {
# Column annotation height
annotColHeight <-
ncol(annotationCol) *
(textheight + unit(2, "bigpts")) +
unit(2, "bigpts")
# Width of the correponding legend
t <- c(as.vector(as.matrix(annotationCol)), colnames(annotationCol))
annotColLegendWidth <- unit(
1.2,
"grobwidth",
textGrob(t[which.max(nchar(t))],
gp = gpar(...)
)
) +
unit(12, "bigpts")
if (!annotationLegend) {
annotColLegendWidth <- unit(0, "npc")
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}
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} else {
annotColHeight <- unit(0, "bigpts")
annotColLegendWidth <- unit(0, "bigpts")
}
# Row annotations
if (!.is.na2(annotationRow)) {
# Row annotation width
annotRowWidth <- ncol(annotationRow) *
(textheight + unit(2, "bigpts")) +
unit(2, "bigpts")
# Width of the correponding legend
t <- c(
as.vector(as.matrix(annotationRow)),
colnames(annotationRow)
)
annotRowLegendWidth <- unit(
1.2,
"grobwidth",
textGrob(t[which.max(nchar(t))],
gp = gpar(...)
)
) +
unit(
12,
"bigpts"
)
if (!annotationLegend) {
annotRowLegendWidth <- unit(0, "npc")
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}
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} else {
annotRowWidth <- unit(0, "bigpts")
annotRowLegendWidth <- unit(0, "bigpts")
}
annotLegendWidth <- max(annotRowLegendWidth, annotColLegendWidth)
# Tree height
treeHeightCol <- unit(treeHeightCol, "bigpts") + unit(5, "bigpts")
treeHeightRow <- unit(treeHeightRow, "bigpts") + unit(5, "bigpts")
# Set cell sizes
if (is.na(cellWidth)) {
matWidth <- unit(1, "npc") -
rownWidth -
legendWidth -
treeHeightRow -
annotRowWidth -
annotLegendWidth
} else {
matWidth <- unit(cellWidth * ncol, "bigpts") +
length(gapsCol) *
unit(0, "bigpts")
}
if (is.na(cellHeight)) {
matHeight <- unit(1, "npc") -
mainHeight -
colnHeight -
treeHeightCol -
annotColHeight
} else {
matHeight <- unit(cellHeight * nrow, "bigpts") +
length(gapsRow) *
unit(0, "bigpts")
}
# Produce gtable
gt <- gtable::gtable(
widths = unit.c(
treeHeightRow,
annotRowWidth,
matWidth,
rownWidth,
legendWidth,
annotLegendWidth
),
heights = unit.c(
mainHeight,
treeHeightCol,
annotColHeight,
matHeight,
colnHeight
),
vp = viewport(gp = do.call(gpar, gp))
)
cw <- convertWidth(matWidth -
(length(gapsCol) * unit(0, "bigpts")),
"bigpts",
valueOnly = TRUE
) / ncol
ch <- convertHeight(matHeight -
(length(gapsRow) * unit(0, "bigpts")),
"bigpts",
valueOnly = TRUE
) / nrow
# Return minimal cell dimension in bigpts to decide if borders are drawn
mindim <- min(cw, ch)
res <- list(gt = gt, mindim = mindim)
return(res)
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}
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.findCoordinates <- function(n, gaps, m = seq(1, n)) {
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if (length(gaps) == 0) {
return(list(
coord = unit(m / n, "npc"),
size = unit(1 / n, "npc")
))
}
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if (max(gaps) > n) {
stop("Gaps do not match with matrix size")
}
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size <- (1 / n) *
(unit(1, "npc") - length(gaps) * unit("0", "bigpts"))
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gaps2 <- base::apply(vapply(
gaps,
function(gap, x) {
x > gap
},
integer(n), m
), 1, sum)
coord <- m * size + (gaps2 * unit("0", "bigpts"))
return(list(coord = coord, size = size))
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}
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.drawDendrogram <- function(hc, gaps, horizontal = TRUE) {
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h <- hc$height / max(hc$height) / 1.05
m <- hc$merge
o <- hc$order
n <- length(o)
m[m > 0] <- n + m[m > 0]
m[m < 0] <- abs(m[m < 0])
dist <- matrix(0,
nrow = 2 * n - 1,
ncol = 2,
dimnames = list(NULL, c("x", "y"))
)
dist[seq(1, n), 1] <- 1 / n / 2 + (1 / n) *
(match(seq(1, n), o) - 1)
for (i in seq(1, nrow(m))) {
dist[n + i, 1] <- (dist[m[i, 1], 1] + dist[m[i, 2], 1]) / 2
dist[n + i, 2] <- h[i]
}
drawConnection <- function(x1, x2, y1, y2, y) {
res <- list(
x = c(x1, x1, x2, x2),
y = c(y1, y, y, y2)
)
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return(res)
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}
x <- rep(NA, nrow(m) * 4)
y <- rep(NA, nrow(m) * 4)
id <- rep(seq(nrow(m)), rep(4, nrow(m)))
for (i in seq(1, nrow(m))) {
c <- drawConnection(
dist[m[i, 1], 1],
dist[m[i, 2], 1],
dist[m[i, 1], 2],
dist[m[i, 2], 2],
h[i]
)
k <- (i - 1) * 4 + 1
x[seq(k, k + 3)] <- c$x
y[seq(k, k + 3)] <- c$y
}
x <- .findCoordinates(n, gaps, x * n)$coord
y <- unit(y, "npc")
if (!horizontal) {
a <- x
x <- unit(1, "npc") - y
y <- unit(1, "npc") - a
}
res <- polylineGrob(x = x, y = y, id = id)
return(res)
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}
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.drawMatrix <- function(matrix,
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borderColor,
gapsRows,
gapsCols,
fmat,
fontSizeNumber,
numberColor) {
n <- nrow(matrix)
m <- ncol(matrix)
coordX <- .findCoordinates(m, gapsCols)
coordY <- .findCoordinates(n, gapsRows)
x <- coordX$coord -
0.5 * coordX$size
y <- unit(1, "npc") -
(coordY$coord - 0.5 * coordY$size)
coord <- expand.grid(y = y, x = x)
res <- gList()
res[["rect"]] <- rectGrob(
x = coord$x,
y = coord$y,
width = coordX$size,
height = coordY$size,
gp = gpar(fill = matrix, col = borderColor)
)
if (attr(fmat, "draw")) {
res[["text"]] <- textGrob(
x = coord$x,
y = coord$y,
label = fmat,
gp = gpar(col = numberColor, fontSize = fontSizeNumber)
)
}
res <- gTree(children = res)
return(res)
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}
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.drawColnames <- function(coln, gaps, ...) {
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coord <- .findCoordinates(length(coln), gaps)
x <- coord$coord - 0.5 * coord$size
res <- textGrob(coln,
x = x,
y = unit(1, "npc") -
unit(3, "bigpts"),
vjust = 0.5,
hjust = 0,
rot = 270,
gp = gpar(...)
)
return(res)
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}
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.drawRownames <- function(rown, gaps, ...) {
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coord <- .findCoordinates(length(rown), gaps)
y <- unit(1, "npc") - (coord$coord - 0.5 * coord$size)
res <- textGrob(rown,
x = unit(3, "bigpts"),
y = y,
vjust = 0.5,
hjust = 0,
gp = gpar(...)
)
return(res)
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}
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.drawLegend <- function(color, breaks, legend, ...) {
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height <- min(unit(1, "npc"), unit(150, "bigpts"))
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legendPos <- (legend - min(breaks)) / (max(breaks) - min(breaks))
legendPos <- height * legendPos + (unit(1, "npc") - height)
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breaks <- (breaks - min(breaks)) / (max(breaks) - min(breaks))
breaks <- height * breaks + (unit(1, "npc") - height)
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h <- breaks[-1] - breaks[-length(breaks)]
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rect <- rectGrob(
x = 0,
y = breaks[-length(breaks)],
width = unit(10, "bigpts"),
height = h,
hjust = 0,
vjust = 0,
gp = gpar(fill = color, col = "#FFFFFF00")
)
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text <- textGrob(names(legend),
x = unit(14, "bigpts"),
y = legendPos,
hjust = 0,
gp = gpar(...)
)
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res <- grobTree(rect, text)
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return(res)
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}
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.convertAnnotations <- function(annotation, annotationColors) {
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new <- annotation
for (i in seq(ncol(annotation))) {
a <- annotation[, i]
b <- annotationColors[[colnames(annotation)[i]]]
if (is.character(a) | is.factor(a)) {
a <- as.character(a)
if (length(setdiff(setdiff(a, NA), names(b))) > 0) {
stop(sprintf(
"Factor levels on variable %s do not match
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with annotationColors",
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colnames(annotation)[i]
))
}
new[, i] <- b[a]
} else {
a <- cut(a, breaks = 100)
new[, i] <- colorRampPalette(b)(100)[a]
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}
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}
return(as.matrix(new))
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}
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.drawAnnotations <- function(convertedAnnotations,
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borderColor,
gaps,
fontSize,
horizontal) {
n <- ncol(convertedAnnotations)
m <- nrow(convertedAnnotations)
coordX <- .findCoordinates(m, gaps)
x <- coordX$coord - 0.5 * coordX$size
# y = cumsum(rep(fontSize, n)) - 4 + cumsum(rep(2, n))
y <- cumsum(rep(fontSize, n)) +
cumsum(rep(2, n)) -
fontSize / 2 + 1
y <- unit(y, "bigpts")
if (horizontal) {
coord <- expand.grid(x = x, y = y)
res <- rectGrob(
x = coord$x,
y = coord$y,
width = coordX$size,
height = unit(fontSize, "bigpts"),
gp = gpar(fill = convertedAnnotations, col = borderColor)
)
} else {
a <- x
x <- unit(1, "npc") - y
y <- unit(1, "npc") - a
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coord <- expand.grid(y = y, x = x)
res <- rectGrob(
x = coord$x,
y = coord$y,
width = unit(fontSize, "bigpts"),
height = coordX$size,
gp = gpar(fill = convertedAnnotations, col = borderColor)
)
}
return(res)
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}
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.drawAnnotationNames <- function(annotations, fontSize, horizontal) {
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n <- ncol(annotations)
x <- unit(3, "bigpts")
y <- cumsum(rep(fontSize, n)) +
cumsum(rep(2, n)) -
fontSize / 2 + 1
y <- unit(y, "bigpts")
if (horizontal) {
res <- textGrob(colnames(annotations),
x = x,
y = y,
hjust = 0,
gp = gpar(fontSize = fontSize, fontface = 2)
)
} else {
a <- x
x <- unit(1, "npc") - y
y <- unit(1, "npc") - a
res <- textGrob(colnames(annotations),
x = x,
y = y,
vjust = 0.5,
hjust = 0,
rot = 270,
gp = gpar(fontSize = fontSize, fontface = 2)
)
}
return(res)
}
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.drawAnnotationLegend <- function(annotation,
annotationColors,
borderColor,
...) {
y <- unit(1, "npc")
textHeight <- unit(
1,
"grobheight",
textGrob("FGH", gp = gpar(...))
)
res <- gList()
for (i in names(annotation)) {
res[[i]] <- textGrob(i,
x = 0,
y = y,
vjust = 1,
hjust = 0,
gp = gpar(fontface = "bold", ...)
)
y <- y - 1.5 * textHeight
if (is.character(annotation[[i]]) |
is.factor(annotation[[i]])) {
n <- length(annotationColors[[i]])
yy <- y - (seq(n) - 1) * 2 * textHeight
res[[paste(i, "r")]] <- rectGrob(
x = unit(0, "npc"),
y = yy,
hjust = 0,
vjust = 1,
height = 2 * textHeight,
width = 2 * textHeight,
gp = gpar(col = borderColor, fill = annotationColors[[i]])
)
res[[paste(i, "t")]] <- textGrob(names(annotationColors[[i]]),
x = textHeight * 2.4,
y = yy - textHeight,
hjust = 0,
vjust = 0.5,
gp = gpar(...)
)
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y <- y - n * 2 * textHeight
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} else {
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yy <- y - 8 * textHeight + seq(0, 1, 0.25)[-1] * 8 * textHeight
h <- 8 * textHeight * 0.25
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res[[paste(i, "r")]] <- rectGrob(
x = unit(0, "npc"),
y = yy,
hjust = 0,
vjust = 1,
height = h,
width = 2 * textHeight,
gp = gpar(
col = NA,
fill = colorRampPalette(annotationColors[[i]])(4)
)
)
res[[paste(i, "r2")]] <- rectGrob(
x = unit(0, "npc"),
y = y,
hjust = 0,
vjust = 1,
height = 8 * textHeight,
width = 2 * textHeight,
gp = gpar(col = borderColor, fill = NA)
)
txt <- rev(range(grid::grid.pretty(range(annotation[[i]],
na.rm = TRUE
))))
yy <- y - c(1, 7) * textHeight
res[[paste(i, "t")]] <- textGrob(txt,
x = textHeight * 2.4,
y = yy,
hjust = 0,
vjust = 0.5,
gp = gpar(...)
)
y <- y - 8 * textHeight
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}
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y <- y - 1.5 * textHeight
}
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res <- gTree(children = res)
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return(res)
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}
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.drawMain <- function(text, ...) {
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res <- textGrob(text, gp = gpar(fontface = "bold", ...))
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return(res)
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}
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vplayout <- function(x, y) {
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return(viewport(layout.pos.row = x, layout.pos.col = y))
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}
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#' @importFrom gtable gtable_height
#' @importFrom gtable gtable_width
#' @importFrom gtable gtable_add_grob
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#' @import grDevices
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.heatmapMotor <- function(matrix,
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borderColor,
cellWidth,
cellHeight,
treeCol,
treeRow,
treeHeightCol,
treeHeightRow,
fileName,
width,
height,
breaks,
color,
legend,
annotationRow,
annotationCol,
annotationColors,
annotationLegend,
annotationNamesRow,
annotationNamesCol,
main,
fontSize,
fontSizeRow,
fontSizeCol,
fmat,
fontSizeNumber,
numberColor,
gapsCol,
gapsRow,
labelsRow,
labelsCol,
...) {
# Set layout
lo <- .lo(
coln = labelsCol,
rown = labelsRow,
nrow = nrow(matrix),
ncol = ncol(matrix),
cellWidth = cellWidth,
cellHeight = cellHeight,
treeHeightCol = treeHeightCol,
treeHeightRow = treeHeightRow,
legend = legend,
annotationCol = annotationCol,
annotationRow = annotationRow,
annotationColors = annotationColors,
annotationLegend = annotationLegend,
annotationNamesRow = annotationNamesRow,
annotationNamesCol = annotationNamesCol,
main = main,
fontSize = fontSize,
fontSizeRow = fontSizeRow,
fontSizeCol = fontSizeCol,
gapsRow = gapsRow,
gapsCol = gapsCol,
...
)
res <- lo$gt
mindim <- lo$mindim
if (!is.na(fileName)) {
if (is.na(height)) {
height <- convertHeight(gtable::gtable_height(res),
"inches",
valueOnly = TRUE
)
}
if (is.na(width)) {
width <- convertWidth(gtable::gtable_width(res),
"inches",
valueOnly = TRUE
)
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}
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# Get file type
r <- regexpr("\\.[a-zA-Z]*$", fileName)
if (r == -1) {
stop("Improper fileName")
}
ending <- substr(
fileName,
r + 1,
r + attr(r, "match.length")
)
f <- switch(ending,
pdf = function(x, ...) {
pdf(x, ...)
},
png = function(x, ...) {
png(x,
units = "in",
res = 300, ...
)
},
jpeg = function(x, ...) {
jpeg(x,
units = "in",
res = 300, ...
)
},
jpg = function(x, ...) {
jpeg(x,
units = "in",
res = 300, ...
)
},
tiff = function(x, ...) {
tiff(x,
units = "in",
res = 300,
compression = "lzw",
...
)
},
bmp = function(x, ...) {
bmp(x,
units = "in",
res = 300, ...
)
},
stop("File type should be: pdf, png, bmp, jpg, tiff")
)
# print(sprintf("height:%f width:%f", height, width))
# gt = .heatmapMotor(matrix,
# cellWidth = cellWidth,
# cellHeight = cellHeight,
# borderColor = borderColor,
# treeCol = treeCol,
# treeRow = treeRow,
# treeHeightCol = treeHeightCol,
# treeHeightRow = treeHeightRow,
# breaks = breaks,
# color = color,
# legend = legend,
# annotationCol = annotationCol,
# annotationRow = annotationRow,
# annotationColors = annotationColors,
# annotationLegend = annotationLegend,
# fileName = NA, main = main,
# fontSize = fontSize,
# fontSizeRow = fontSizeRow,
# fontSizeCol = fontSizeCol,
# fmat = fmat,
# fontSizeNumber = fontSizeNumber,
# numberColor = numberColor,
# labelsRow = labelsRow,
# labelsCol = labelsCol,
# gapsCol = gapsCol,
# gapsRow = gapsRow, ...)
f(fileName, height = height, width = width)
gt <- .heatmapMotor(matrix,
cellWidth = cellWidth,
cellHeight = cellHeight,
borderColor = borderColor,
treeCol = treeCol,
treeRow = treeRow,
treeHeightCol = treeHeightCol,
treeHeightRow = treeHeightRow,
breaks = breaks,
color = color,
legend = legend,
annotationCol = annotationCol,
annotationRow = annotationRow,
annotationColors = annotationColors,
annotationLegend = annotationLegend,
annotationNamesRow = annotationNamesRow,
annotationNamesCol = annotationNamesCol,
fileName = NA,
main = main,
fontSize = fontSize,
fontSizeRow = fontSizeRow,
fontSizeCol = fontSizeCol,
fmat = fmat,
fontSizeNumber = fontSizeNumber,
numberColor = numberColor,
labelsRow = labelsRow,
labelsCol = labelsCol,
gapsCol = gapsCol,
gapsRow = gapsRow,
...
)
grid.draw(gt)
dev.off()
return(gt)
}
# Omit border color if cell size is too small
if (mindim < 3) {
borderColor <- NA
}
# Draw title
if (!is.na(main)) {
elem <- .drawMain(main, fontSize = 1.3 * fontSize, ...)
res <- gtable::gtable_add_grob(res,
elem,
t = 1,
l = 3,
name = "main",
clip = "off"
)
}
# Draw tree for the columns
if (!.is.na2(treeCol) & treeHeightCol != 0) {
elem <- .drawDendrogram(treeCol, gapsCol, horizontal = TRUE)
res <- gtable::gtable_add_grob(res,
elem,
t = 2,
l = 3,
name = "col_tree"
)
}
# Draw tree for the rows
if (!.is.na2(treeRow) & treeHeightRow != 0) {
elem <- .drawDendrogram(treeRow, gapsRow, horizontal = FALSE)
res <- gtable::gtable_add_grob(res,
elem,
t = 4,
l = 1,
name = "row_tree"
)
}
# Draw matrix
elem <- .drawMatrix(
matrix,
borderColor,
gapsRow,
gapsCol,
fmat,
fontSizeNumber,
numberColor
)
res <- gtable::gtable_add_grob(res,
elem,
t = 4,
l = 3,
clip = "off",
name = "matrix"
)
# Draw colnames
if (length(labelsCol) != 0) {
pars <- list(labelsCol,
gaps = gapsCol,
fontSize = fontSizeCol,
...
)
elem <- do.call(.drawColnames, pars)
res <- gtable::gtable_add_grob(res,
elem,
t = 5,
l = 3,
clip = "off",
name = "col_names"
)
}
# Draw rownames
if (length(labelsRow) != 0) {
pars <- list(labelsRow,
gaps = gapsRow,
fontSize = fontSizeRow, ...
)
elem <- do.call(.drawRownames, pars)
res <- gtable::gtable_add_grob(res,
elem,
t = 4,
l = 4,
clip = "off",
name = "row_names"
)
}
# Draw annotation tracks on cols
if (!.is.na2(annotationCol)) {
# Draw tracks
convertedAnnotation <- .convertAnnotations(
annotationCol,
annotationColors
)
elem <- .drawAnnotations(convertedAnnotation,
borderColor,
gapsCol,
fontSize,
horizontal = TRUE
)
res <- gtable::gtable_add_grob(res,
elem,
t = 3,
l = 3,
clip = "off",
name = "col_annotation"
)
# Draw names
if (annotationNamesCol) {
elem <- .drawAnnotationNames(annotationCol,
fontSize,
horizontal = TRUE
)
res <- gtable::gtable_add_grob(res,
elem,
t = 3,
l = 4,
clip = "off",
name = "col_annotation_names"
)
}
}
# Draw annotation tracks on rows
if (!.is.na2(annotationRow)) {
# Draw tracks
convertedAnnotation <- .convertAnnotations(
annotationRow,
annotationColors
)
elem <- .drawAnnotations(convertedAnnotation,
borderColor,
gapsRow,
fontSize,
horizontal = FALSE
)
res <- gtable::gtable_add_grob(res,
elem,
t = 4,
l = 2,
clip = "off",
name = "row_annotation"
)
# Draw names
if (annotationNamesRow) {
elem <- .drawAnnotationNames(annotationRow,
fontSize,
horizontal = FALSE
)
res <- gtable::gtable_add_grob(res,
elem,
t = 5,
l = 2,
clip = "off",
name = "row_annotation_names"
)
|
| ae4c10aa |
}
|
| f2a1c1ba |
}
# Draw annotation legend
annotation <- c(
annotationCol[seq(length(annotationCol), 1)],
annotationRow[seq(length(annotationRow), 1)]
)
annotation <- annotation[unlist(lapply(
annotation,
function(x) !.is.na2(x)
))]
if (length(annotation) > 0 & annotationLegend) {
elem <- .drawAnnotationLegend(annotation,
annotationColors,
borderColor,
fontSize = fontSize,
...
)
t <- ifelse(is.null(labelsRow), 4, 3)
res <- gtable::gtable_add_grob(res,
elem,
t = t,
l = 6,
b = 5,
clip = "off",
name = "annotationLegend"
)
}
# Draw legend
if (!.is.na2(legend)) {
elem <- .drawLegend(color, breaks, legend, fontSize = fontSize, ...)
t <- ifelse(is.null(labelsRow), 4, 3)
res <- gtable::gtable_add_grob(res,
elem,
t = t,
l = 5,
b = 5,
clip = "off",
name = "legend"
)
}
return(res)
}
|
| b26d22a2 |
|
| f2a1c1ba |
.generateBreaks <- function(x, n, center = FALSE) {
if (center) {
m <- max(abs(c(
min(x, na.rm = TRUE),
max(x, na.rm = TRUE)
)))
res <- seq(-m, m, length.out = n + 1)
} else {
res <- seq(min(x, na.rm = TRUE),
max(x, na.rm = TRUE),
length.out = n + 1
)
}
return(res)
|
| ae4c10aa |
}
|
| 9c6ba642 |
.scaleVecColours <- function(x, col = rainbow(10), breaks = NA) {
|
| f2a1c1ba |
return(col[as.numeric(cut(x, breaks = breaks, include.lowest = TRUE))])
|
| ae4c10aa |
}
|
| 9c6ba642 |
.scaleColours <- function(mat,
|
| f2a1c1ba |
col = rainbow(10),
breaks = NA) {
mat <- as.matrix(mat)
return(matrix(
.scaleVecColours(as.vector(mat), col = col, breaks = breaks),
nrow(mat),
ncol(mat),
dimnames = list(rownames(mat), colnames(mat))
))
|
| ae4c10aa |
}
|
| b26d22a2 |
## changed the original clusterMat() in the pheatmap.r
|
| 7890fdf1 |
#' @importFrom scales hue_pal
|
| 9c6ba642 |
.clusterMat <- function(mat, labels, distance, method) {
|
| f2a1c1ba |
# this funciton is going to change the .clusterMat() in pheatmap
if (!(method %in% c(
"ward.D",
"ward.D2",
"ward",
"single",
"complete",
"average",
"mcquitty",
"median",
"centroid"
))) {
stop("clustering method has to one form the list:
|
| b26d22a2 |
'ward',
'ward.D',
'ward.D2',
'single',
'complete',
'average',
'mcquitty',
'median'
or 'centroid'.")
|
| f2a1c1ba |
}
class.label <- unique(labels)
nGroup <- length(class.label) # [#group]
# get "hclust" object for each group then wrap them up as group.hclust
# distance function preparation
dis <- function(mat, distance) {
if (!(distance[1] %in% c(
"correlation",
"euclidean",
"maximum",
"manhattan",
"canberra",
"binary",
"minkowski"
)) &
!methods::is(distance, "dist")) {
stop(
"distance has to be a dissimilarity structure as produced by",
" dist or one measure form the list: 'correlation',",
" 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary',",
" 'minkowski'"
)
|
| ae4c10aa |
}
|
| b26d22a2 |
|
| f2a1c1ba |
if (distance[1] == "correlation") {
# this part should be confirmed whether being wrong?
# ToDo: how is the correlation matrix converted to a dsit matrix
d <- stats::as.dist(1 - stats::cor(t(mat)))
} else {
d <- stats::dist(mat, method = distance)
|
| ae4c10aa |
}
|
| b26d22a2 |
|
| f2a1c1ba |
return(d)
}
|
| b26d22a2 |
|
| f2a1c1ba |
# initiate the final returning value: a "hclust" object
cum.hclust <- list()
|
| b26d22a2 |
|
| f2a1c1ba |
if (nGroup == 1) {
# matrix has only 1 group
if (length(labels) == 1) {
stop("only one row/column for the matrix")
}
group.hclust <- stats::hclust(dis(
mat = mat,
distance = distance
),
method = method
)
cum.hclust <- group.hclust
} else {
# matrix has more than 1 groups
group.hclust <- vapply(
class.label, function(x) {
# get the positions of class label
class.pos <- which(labels == x)
if (length(class.pos) == 1) {
# if only 1 row in the group return a manually made "hclust"
# object
sub.hclust <- as.list(seq(7))
names(sub.hclust) <- c(
"merge",
"height",
"order",
"labels",
"method",
"call",
"dist.method"
)
class(sub.hclust) <- "hclust"
sub.hclust$merge <- matrix(c(0, 0), nrow = 1)
sub.hclust$height <- 0
sub.hclust$order <- 1
return(sub.hclust)
} else if (length(class.pos) > 1) {
# if >1 rows return the "hclust" object
return(stats::hclust(dis(
mat = mat[class.pos, ],
distance = distance
),
method = method
))
}
},
list(
"merge" = 0,
"height" = 0,
"order" = 0,
"labels" = 0,
"method" = 0,
"call" = 0,
"dist.method" = 0
)
)
# the length(group.hclust) is the [#group] == nGroup ,
# group.hclust[[i]] to get each "hclust"
# then modify the "hclust" object and get them merged into one
# "hclust" object
# initiate the final "hclust" object
cum.hclust <- group.hclust[, nGroup]
# merge function preparation
mergeHclust <- function(hclust1, hclust2) {
# "hclust" object modifying function preparation
if (hclust1$merge[1, 1] == 0 &
hclust2$merge[1, 1] == 0) {
# both groups have only 1 row
hclustCom <- as.list(seq(7))
names(hclustCom) <-
c(
"merge",
"height",
"order",
"labels",
"method",
"call",
"dist.method"
)
class(hclustCom) <- "hclust"
hclustCom$merge <- matrix(c(-1, -2), nrow = 1)
# check for different matrix whether 1 should be good
hclustCom$height <- 1
hclustCom$order <- c(1, 2)
return(hclustCom)
} else if (hclust1$merge[1, 1] != 0 &
hclust2$merge[1, 1] != 0) {
# both group have >1 rows
# nodes in the hclust1 group, so actually the #rows should
# be dim()[1]+1
row.1 <- dim(hclust1$merge)[1]
# nodes in the hclust2 group
row.2 <- dim(hclust2$merge)[1]
hclustCom <- list()
mer <- hclust2$merge
# modify the hclust2$merge matrix
hclustCom$merge <- (mer > 0) *
(mer + row.1) + (mer < 0) *
(mer - row.1 - 1)
# combine the merge matrix from the 2 groups
hclustCom$merge <- rbind(
hclust1$merge,
hclustCom$merge
)
hclustCom$merge <- rbind(
hclustCom$merge,
c(row.1, row.1 + row.2)
)
hclustCom$height <- c(hclust1$height, hclust2$height)
# check for different matrix whether 1 should be good
hclustCom$height <- c(
hclustCom$height,
max(hclustCom$height) + 1
)
hclustCom$order <- c(
hclust1$order,
hclust2$order + row.1 + 1
)
class(hclustCom) <- "hclust"
} else {
# one group has only 1 row, the other group has >1 rows
if (hclust1$merge[1, 1] == 0) {
# hclust1 has 1 row , hclust2 has >1 rows
# nodes in the hclust2 group
row.2 <- dim(hclust2$merge)[1]
hclustCom <- as.list(seq(7))
names(hclustCom) <- c(
"merge",
"height",
"order",
"labels",
"method",
"call",
"dist.method"
)
class(hclustCom) <- "hclust"
mer <- hclust2$merge
hclustCom$merge <- (mer > 0) *
(mer) +
(mer < 0) *
(mer - 1)
hclustCom$merge <- rbind(
hclustCom$merge,
c(-1, row.2)
)
# check for different matrix whether 1 should be good
hclustCom$height <- c(
hclust2$height,
max(hclust2$height) + 1
)
hclustCom$order <- c(1, hclust2$order + 1)
} else if (hclust2$merge[1, 1] == 0) {
# the hclust1 has >1 rows , and hclust2 has 1 row
# nodes in the hclust1 group
row.1 <- dim(hclust1$merge)[1]
hclustCom <- as.list(seq(1, 7))
names(hclustCom) <-
c(
"merge",
"height",
"order",
"labels",
"method",
"call",
"dist.method"
)
class(hclustCom) <- "hclust"
hclustCom$merge <- hclust1$merge
hclustCom$merge <- rbind(
hclustCom$merge,
c(row.1, - (row.1 + 2))
)
hclustCom$height <- c(
hclust1$height,
max(hclust1$height) + 1
)
hclustCom$order <- c(
hclust1$order,
max(hclust1$order) + 1
)
|
| b26d22a2 |
}
|
| f2a1c1ba |
}
return(hclustCom)
|
| ae4c10aa |
}
|
| b26d22a2 |
|
| f2a1c1ba |
# merge the "hclust" object into the final one "hclust" object
for (i in seq(nGroup - 1, 1, -1)) {
cum.hclust <- mergeHclust(group.hclust[, i], cum.hclust)
}
}
cum.hclust$labels <- NULL
cum.hclust$call <- NULL
cum.hclust$method <- NULL
cum.hclust$dist.method <- NULL
|
| b26d22a2 |
|
| f2a1c1ba |
return(cum.hclust)
|
| ae4c10aa |
}
|
| 9c6ba642 |
.scaleRows <- function(x) {
|
| f2a1c1ba |
m <- base::apply(x, 1, mean, na.rm = TRUE)
s <- base::apply(x, 1, stats::sd, na.rm = TRUE)
return((x - m) / s)
|
| ae4c10aa |
}
|
| 9c6ba642 |
.scaleMat <- function(mat, scale) {
|
| f2a1c1ba |
if (!(scale %in% c("none", "row", "column"))) {
stop("scale argument shoud take values: 'none', 'row' or 'column'")
}
mat <- switch(scale,
none = mat,
row = .scaleRows(mat),
column = t(.scaleRows(t(mat)))
)
return(mat)
|
| ae4c10aa |
}
|
| d7196f24 |
#' @importFrom scales dscale
|
| e3638ca1 |
#' @importFrom scales brewer_pal
|
| 2c8e7d4d |
.generateAnnotationColours <- function(annotation,
|
| f2a1c1ba |
annotationColors,
drop) {
if (.is.na2(annotationColors)) {
annotationColors <- list()
}
count <- 0
for (i in seq(length(annotation))) {
annotation[[i]] <- annotation[[i]][!is.na(annotation[[i]])]
if (is.character(annotation[[i]]) |
is.factor(annotation[[i]])) {
if (is.factor(annotation[[i]]) & !drop) {
count <- count + length(levels(annotation[[i]]))
} else {
count <- count + length(unique(annotation[[i]]))
}
}
}
factorColors <- scales::dscale(
factor(seq(1, count)),
scales::hue_pal(l = 75)
)
contCounter <- 2
for (i in seq(length(annotation))) {
if (!(names(annotation)[i] %in% names(annotationColors))) {
if (is.character(annotation[[i]]) |
is.factor(annotation[[i]])) {
n <- length(unique(annotation[[i]]))
if (is.factor(annotation[[i]]) & !drop) {
n <- length(levels(annotation[[i]]))
|
| b26d22a2 |
}
|
| f2a1c1ba |
ind <- sample(seq_along(factorColors), n)
annotationColors[[names(annotation)[i]]] <-
factorColors[ind]
l <- levels(as.factor(annotation[[i]]))
l <- l[l %in% unique(annotation[[i]])]
if (is.factor(annotation[[i]]) & !drop) {
l <- levels(annotation[[i]])
|
| ae4c10aa |
}
|
| f2a1c1ba |
names(annotationColors[[names(annotation)[i]]]) <- l
factorColors <- factorColors[-ind]
} else {
annotationColors[[names(annotation)[i]]] <-
scales::brewer_pal("seq", contCounter)(5)[seq(4)]
contCounter <- contCounter + 1
}
|
| ae4c10aa |
}
|
| f2a1c1ba |
}
return(annotationColors)
}
|
| ae4c10aa |
|
| b26d22a2 |
|
| 9c6ba642 |
.findGaps <- function(tree, cutreeN) {
|
| f2a1c1ba |
v <- stats::cutree(tree, cutreeN)[tree$order]
gaps <- which((v[-1] - v[-length(v)]) != 0)
return(gaps)
|
| ae4c10aa |
}
|
| 9c6ba642 |
.is.na2 <- function(x) {
|
| f2a1c1ba |
if (is.list(x) | length(x) > 1) {
return(FALSE)
}
if (length(x) == 0) {
return(TRUE)
}
return(is.na(x))
|
| ae4c10aa |
}
|
| 9c6ba642 |
.identity2 <- function(x, ...) {
|
| f2a1c1ba |
return(x)
|
| ae4c10aa |
}
|
| ca5fb59d |
#' @title A function to draw clustered heatmaps.
#' @description A function to draw clustered heatmaps where one has better
#' control over some graphical parameters such as cell size, etc.
|
| ae4c10aa |
#'
|
| ca5fb59d |
#' The function also allows to aggregate the rows using kmeans clustering.
#' This is advisable if number of rows is so big that R cannot handle their
#' hierarchical clustering anymore, roughly more than 1000. Instead of showing
#' all the rows separately one can cluster the rows in advance and show only
#' the cluster centers. The number of clusters can be tuned with parameter
#' kmeansK.
|
| ae4c10aa |
#' @param mat numeric matrix of the values to be plotted.
#' @param color vector of colors used in heatmap.
|
| ca5fb59d |
#' @param kmeansK the number of kmeans clusters to make, if we want to
#' agggregate the rows before drawing heatmap. If NA then the rows are not
#' aggregated.
#' @param breaks Numeric vector. A sequence of numbers that covers the range
#' of values in the normalized `counts`. Values in the normalized `matrix` are
#' assigned to each bin in `breaks`. Each break is assigned to a unique color
#' from `col`. If NULL, then breaks are calculated automatically. Default NULL.
#' @param borderColor color of cell borders on heatmap, use NA if no border
#' should be drawn.
#' @param cellWidth individual cell width in points. If left as NA, then the
#' values depend on the size of plotting window.
#' @param cellHeight individual cell height in points. If left as NA, then the
#' values depend on the size of plotting window.
#' @param scale character indicating if the values should be centered and
#' scaled in either the row direction or the column direction, or none.
#' Corresponding values are \code{"row"}, \code{"column"} and \code{"none"}.
#' @param clusterRows boolean values determining if rows should be clustered or
#' \code{hclust} object,
#' @param clusterCols boolean values determining if columns should be clustered
#' or \code{hclust} object.
#' @param clusteringDistanceRows distance measure used in clustering rows.
#' Possible values are \code{"correlation"} for Pearson correlation and all
#' the distances supported by \code{\link{dist}}, such as \code{"euclidean"},
#' etc. If the value is none of the above it is assumed that a distance matrix
#' is provided.
#' @param clusteringDistanceCols distance measure used in clustering columns.
#' Possible values the same as for clusteringDistanceRows.
|
| b26d22a2 |
#' @param clusteringMethod clustering method used. Accepts the same values as
|
| ca5fb59d |
#' \code{\link{hclust}}.
|
| b26d22a2 |
#' @param clusteringCallback callback function to modify the clustering. Is
|
| ca5fb59d |
#' called with two parameters: original \code{hclust} object and the matrix
#' used for clustering. Must return a \code{hclust} object.
|
| b26d22a2 |
#' @param cutreeRows number of clusters the rows are divided into, based on the
#' hierarchical clustering (using cutree), if rows are not clustered, the
|
| ca5fb59d |
#' argument is ignored
|
| b26d22a2 |
#' @param cutreeCols similar to \code{cutreeRows}, but for columns
#' @param treeHeightRow the height of a tree for rows, if these are clustered.
|
| ca5fb59d |
#' Default value 50 points.
#' @param treeHeightCol the height of a tree for columns, if these are
#' clustered. Default value 50 points.
|
| ae4c10aa |
#' @param legend logical to determine if legend should be drawn or not.
|
| b26d22a2 |
#' @param legendBreaks vector of breakpoints for the legend.
#' @param legendLabels vector of labels for the \code{legendBreaks}.
#' @param annotationRow data frame that specifies the annotations shown on left
#' side of the heatmap. Each row defines the features for a specific row. The
|
| ca5fb59d |
#' rows in the data and in the annotation are matched using corresponding row
|
| ae4c10aa |
#' names. Note that color schemes takes into account if variable is continuous
#' or discrete.
|
| b26d22a2 |
#' @param annotationCol similar to annotationRow, but for columns.
|
| ca5fb59d |
#' @param annotation deprecated parameter that currently sets the annotationCol
#' if it is missing.
|
| b26d22a2 |
#' @param annotationColors list for specifying annotationRow and
|
| ca5fb59d |
#' annotationCol track colors manually. It is possible to define the colors
#' for only some of the features. Check examples for details.
|
| b26d22a2 |
#' @param annotationLegend boolean value showing if the legend for annotation
|
| ca5fb59d |
#' tracks should be drawn.
#' @param annotationNamesRow boolean value showing if the names for row
#' annotation tracks should be drawn.
#' @param annotationNamesCol boolean value showing if the names for column
#' annotation tracks should be drawn.
|
| b26d22a2 |
#' @param dropLevels logical to determine if unused levels are also shown in
|
| ca5fb59d |
#' the legend.
|
| b26d22a2 |
#' @param showRownames boolean specifying if column names are be shown.
#' @param showColnames boolean specifying if column names are be shown.
|
| ae4c10aa |
#' @param main the title of the plot
|
| b26d22a2 |
#' @param fontSize base fontsize for the plot
#' @param fontSizeRow fontsize for rownames (Default: fontsize)
#' @param fontSizeCol fontsize for colnames (Default: fontsize)
|
| ca5fb59d |
#' @param displayNumbers logical determining if the numeric values are also
#' printed to the cells. If this is a matrix (with same dimensions as original
#' matrix), the contents of the matrix are shown instead of original values.
#' @param numberFormat format strings (C printf style) of the numbers shown in
#' cells. For example "\code{\%.2f}" shows 2 decimal places and "\code{\%.1e}"
#' shows exponential notation (see more in \code{\link{sprintf}}).
|
| b26d22a2 |
#' @param numberColor color of the text
#' @param fontSizeNumber fontsize of the numbers displayed in cells
#' @param gapsRow vector of row indices that show shere to put gaps into
#' heatmap. Used only if the rows are not clustered. See \code{cutreeRow}
#' to see how to introduce gaps to clustered rows.
#' @param gapsCol similar to gapsRow, but for columns.
#' @param labelsRow custom labels for rows that are used instead of rownames.
#' @param labelsCol similar to labelsRow, but for columns.
#' @param fileName file path where to save the picture. Filetype is decided by
|
| ca5fb59d |
#' the extension in the path. Currently following formats are supported: png,
#' pdf, tiff, bmp, jpeg. Even if the plot does not fit into the plotting
#' window, the file size is calculated so that the plot would fit there,
#' unless specified otherwise.
|
| ae4c10aa |
#' @param width manual option for determining the output file width in inches.
#' @param height manual option for determining the output file height in inches.
#' @param silent do not draw the plot (useful when using the gtable output)
|
| b26d22a2 |
#' @param rowLabel row cluster labels for semi-clustering
#' @param colLabel column cluster labels for semi-clustering
|
| 8f1edfa3 |
#' @param rowGroupOrder Vector. Specifies the order of feature clusters when
|
| c4f248cb |
#' semisupervised clustering is performed on the \code{y} labels.
|
| 8f1edfa3 |
#' @param colGroupOrder Vector. Specifies the order of cell clusters when
|
| c4f248cb |
#' semisupervised clustering is performed on the \code{z} labels.
|
| ca5fb59d |
#' @param \dots graphical parameters for the text used in plot. Parameters
#' passed to \code{\link{grid.text}}, see \code{\link{gpar}}.
|
| b26d22a2 |
#' @return
#' Invisibly a list of components
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| ae4c10aa |
#' \itemize{
|
| ca5fb59d |
#' \item \code{treeRow} the clustering of rows as \code{\link{hclust}}
#' object
#' \item \code{treeCol} the clustering of columns as \code{\link{hclust}}
#' object
#' \item \code{kmeans} the kmeans clustering of rows if parameter
#' \code{kmeansK} was specified
|
| ae4c10aa |
#' }
#' @author Raivo Kolde <rkolde@@gmail.com>
#' #@examples
#' # Create test matrix
#' test = matrix(rnorm(200), 20, 10)
|
| ca5fb59d |
#' test[seq(10), seq(1, 10, 2)] = test[seq(10), seq(1, 10, 2)] + 3
#' test[seq(11, 20), seq(2, 10, 2)] = test[seq(11, 20), seq(2, 10, 2)] + 2
#' test[seq(15, 20), seq(2, 10, 2)] = test[seq(15, 20), seq(2, 10, 2)] + 4
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| 92ca710a |
#' colnames(test) = paste("Test", seq(10), sep = "")
#' rownames(test) = paste("Gene", seq(20), sep = "")
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| b26d22a2 |
#'
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| ae4c10aa |
#' # Draw heatmaps
#' pheatmap(test)
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| b26d22a2 |
#' pheatmap(test, kmeansK = 2)
#' pheatmap(test, scale = "row", clusteringDistanceRows = "correlation")
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| ca5fb59d |
#' pheatmap(test, color = colorRampPalette(c("navy",
#' "white", "firebrick3"))(50))
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| ae4c10aa |
#' pheatmap(test, cluster_row = FALSE)
#' pheatmap(test, legend = FALSE)
|
| b26d22a2 |
#'
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| ae4c10aa |
#' # Show text within cells
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| b26d22a2 |
#' pheatmap(test, displayNumbers = TRUE)
#' pheatmap(test, displayNumbers = TRUE, numberFormat = "\%.1e")
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| ca5fb59d |
#' pheatmap(test, displayNumbers = matrix(ifelse(test > 5,
#' "*", ""), nrow(test)))
#' pheatmap(test, cluster_row = FALSE,
#' legendBreaks = seq(-1, 4), legendLabels = c("0",
#' "1e-4", "1e-3", "1e-2", "1e-1", "1"))
|
| b26d22a2 |
#'
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| ae4c10aa |
#' # Fix cell sizes and save to file with correct size
|
| b26d22a2 |
#' pheatmap(test, cellWidth = 15, cellHeight = 12, main = "Example heatmap")
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| ca5fb59d |
#' pheatmap(test, cellWidth = 15, cellHeight = 12, fontSize = 8,
#' fileName = "test.pdf")
|
| b26d22a2 |
#'
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| ae4c10aa |
#' # Generate annotations for rows and columns
|
| ca5fb59d |
#' annotationCol = data.frame(CellType = factor(rep(c("CT1", "CT2"), 5)),
#' Time = seq(5))
#' rownames(annotationCol) = paste("Test", seq(10), sep = "")
|
| b26d22a2 |
#'
#' annotationRow = data.frame(GeneClass = factor(rep(c("Path1",
|
| ca5fb59d |
#' "Path2",
#' "Path3"),
#' c(10, 4, 6))))
#' rownames(annotationRow) = paste("Gene", seq(20), sep = "")
|
| b26d22a2 |
#'
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| ae4c10aa |
#' # Display row and color annotations
|
| b26d22a2 |
#' pheatmap(test, annotationCol = annotationCol)
#' pheatmap(test, annotationCol = annotationCol, annotationLegend = FALSE)
#' pheatmap(test, annotationCol = annotationCol, annotationRow = annotationRow)
#'
|
| ae4c10aa |
#' # Specify colors
|
| b26d22a2 |
#' ann_colors = list(Time = c("white", "firebrick"),
|
| ae4c10aa |
#' CellType = c(CT1 = "#1B9E77", CT2 = "#D95F02"),
|
| b26d22a2 |
#' GeneClass = c(Path1 = "#7570B3", Path2 = "#E7298A", Path3 = "#66A61E"))
#'
|
| ca5fb59d |
#' pheatmap(test, annotationCol = annotationCol, annotationColors = ann_colors,
#' main = "Title")
|
| b26d22a2 |
#' pheatmap(test, annotationCol = annotationCol, annotationRow = annotationRow,
|
| ca5fb59d |
#' annotationColors = ann_colors)
#' pheatmap(test, annotationCol = annotationCol,
#' annotationColors = ann_colors[2])
|
| b26d22a2 |
#'
|
| ae4c10aa |
#' # Gaps in heatmaps
|
| ca5fb59d |
#' pheatmap(test, annotationCol = annotationCol, clusterRows = FALSE,
#' gapsRow = c(10, 14))
#' pheatmap(test, annotationCol = annotationCol, clusterRows = FALSE,
#' gapsRow = c(10, 14), cutreeCol = 2)
|
| b26d22a2 |
#'
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| ae4c10aa |
#' # Show custom strings as row/col names
|
| b26d22a2 |
#' labelsRow = c("", "", "", "", "", "", "", "", "", "", "", "", "", "", "",
|
| ae4c10aa |
#' "", "", "Il10", "Il15", "Il1b")
|
| b26d22a2 |
#'
#' pheatmap(test, annotationCol = annotationCol, labelsRow = labelsRow)
#'
|
| ae4c10aa |
#' # Specifying clustering from distance matrix
#' drows = stats::dist(test, method = "minkowski")
#' dcols = stats::dist(t(test), method = "minkowski")
|
| b26d22a2 |
#' pheatmap(test,
#' clusteringDistanceRows = drows,
#' clusteringDistanceCols = dcols)
#'
|
| ae4c10aa |
#' # Modify ordering of the clusters using clustering callback option
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| 926f61e5 |
#' callback = function(hc, mat) {
|
| ca5fb59d |
#' sv = svd(t(mat))$v[, 1]
|
| ae4c10aa |
#' dend = reorder(as.dendrogram(hc), wts = sv)
#' as.hclust(dend)
#' }
|
| b26d22a2 |
#'
#' pheatmap(test, clusteringCallback = callback)
|
| 7890fdf1 |
#' @importFrom grid grid.pretty
|
| d7196f24 |
#' @importFrom RColorBrewer brewer.pal
|
| b26d22a2 |
semiPheatmap <- function(mat,
|
| f2a1c1ba |
color = colorRampPalette(
rev(brewer.pal(n = 7,
name = "RdYlBu")))(100),
kmeansK = NA,
breaks = NA,
borderColor = "grey60",
cellWidth = NA,
cellHeight = NA,
scale = "none",
clusterRows = TRUE,
clusterCols = TRUE,
clusteringDistanceRows = "euclidean",
clusteringDistanceCols = "euclidean",
clusteringMethod = "complete",
clusteringCallback = .identity2,
cutreeRows = NA,
cutreeCols = NA,
treeHeightRow = ifelse(clusterRows, 50, 0),
treeHeightCol = ifelse(clusterCols, 50, 0),
legend = TRUE,
legendBreaks = NA,
legendLabels = NA,
annotationRow = NA,
annotationCol = NA,
annotation = NA,
annotationColors = NA,
annotationLegend = TRUE,
annotationNamesRow = TRUE,
annotationNamesCol = TRUE,
dropLevels = TRUE,
showRownames = TRUE,
showColnames = TRUE,
main = NA,
fontSize = 10,
fontSizeRow = fontSize,
fontSizeCol = fontSize,
displayNumbers = FALSE,
numberFormat = "%.2f",
numberColor = "grey30",
fontSizeNumber = 0.8 * fontSize,
gapsRow = NULL,
gapsCol = NULL,
labelsRow = NULL,
labelsCol = NULL,
fileName = NA,
width = NA,
height = NA,
silent = FALSE,
rowLabel,
colLabel,
rowGroupOrder = NULL,
colGroupOrder = NULL,
...) {
# Set labels
if (is.null(labelsRow) & !is.null(rownames(mat))) {
labelsRow <- rownames(mat)
}
if (is.null(labelsRow) & is.null(rownames(mat))) {
labelsRow <- seq(nrow(mat))
rownames(mat) <- seq(nrow(mat))
}
|
| b26d22a2 |
|
| f2a1c1ba |
if (is.null(labelsCol) & !is.null(colnames(mat))) {
labelsCol <- colnames(mat)
}
if (is.null(labelsCol) & is.null(colnames(mat))) {
labelsCol <- seq(ncol(mat))
colnames(mat) <- seq(ncol(mat))
}
if (.is.na2(breaks)) {
breaks <- .generateBreaks(mat, length(color), center = TRUE)
}
# Kmeans
if (!is.na(kmeansK)) {
# Cluster data
km <- stats::kmeans(mat, kmeansK, iter.max = 100)
mat <- km$centers
# Compose rownames
t <- table(km$cluster)
labelsRow <- sprintf("Cluster: %s Size: %d", names(t), t)
} else {
km <- NA
}
# Format numbers to be displayed in cells
if (is.matrix(displayNumbers) | is.data.frame(displayNumbers)) {
if (nrow(displayNumbers) != nrow(mat) |
ncol(displayNumbers) != ncol(mat)) {
stop("If displayNumbers provided as matrix,
its dimensions have to match with mat")
|
| ae4c10aa |
}
|
| b26d22a2 |
|
| f2a1c1ba |
displayNumbers <- as.matrix(displayNumbers)
fmat <- matrix(as.character(displayNumbers),
nrow = nrow(displayNumbers),
ncol = ncol(displayNumbers)
)
fmatDraw <- TRUE
} else {
if (displayNumbers) {
fmat <- matrix(sprintf(numberFormat, mat),
nrow = nrow(mat),
ncol = ncol(mat)
)
fmatDraw <- TRUE
|
| b26d22a2 |
} else {
|
| f2a1c1ba |
fmat <- matrix(NA, nrow = nrow(mat), ncol = ncol(mat))
fmatDraw <- FALSE
|
| ae4c10aa |
}
|
| f2a1c1ba |
}
|
| b26d22a2 |
|
| f2a1c1ba |
# Do clustering for rows
if (isTRUE(clusterRows)) {
if (is.null(rowLabel)) {
rowLabel <- rep(1, nrow(mat))
|
| b26d22a2 |
} else {
|
| f2a1c1ba |
# o <- order(rowLabel)
o <- .Order(labels = rowLabel, groupOrder = rowGroupOrder)
mat <- mat[o, , drop = FALSE]
fmat <- fmat[o, , drop = FALSE]
rowLabel <- rowLabel[o]
if (!is.null(annotationRow) && !is.null(ncol(annotationRow))) {
annotationRow <- annotationRow[o, , drop = FALSE]
}
|
| ae4c10aa |
}
|
| f2a1c1ba |
treeRow <- .clusterMat(mat,
rowLabel,
distance = clusteringDistanceRows,
method = clusteringMethod
)
treeRow <- clusteringCallback(treeRow, mat)
mat <- mat[treeRow$order, , drop = FALSE]
fmat <- fmat[treeRow$order, , drop = FALSE]
labelsRow <- labelsRow[treeRow$order]
if (!is.null(annotationRow) && !is.null(ncol(annotationRow))) {
annotationRow <- annotationRow[treeRow$order, , drop = FALSE]
}
if (!is.na(cutreeRows)) {
gapsRow <- .findGaps(treeRow, cutreeRows)
|
| ae4c10aa |
} else {
|
| f2a1c1ba |
gapsRow <- NULL
|
| b26d22a2 |
}
|
| f2a1c1ba |
} else {
treeRow <- NA
treeHeightRow <- 0
}
|
| b26d22a2 |
|
| f2a1c1ba |
## Do clustering for columns
if (isTRUE(clusterCols)) {
if (is.null(colLabel)) {
colLabel <- rep(1, ncol(mat))
|
| ae4c10aa |
} else {
|
| f2a1c1ba |
# o <- order(colLabel)
o <- .Order(labels = colLabel, groupOrder = colGroupOrder)
mat <- mat[, o, drop = FALSE]
fmat <- fmat[, o, drop = FALSE]
colLabel <- colLabel[o]
if (!is.null(annotationCol) && !is.null(ncol(annotationCol))) {
annotationCol <- annotationCol[o, , drop = FALSE]
}
|
| b26d22a2 |
}
|
| f2a1c1ba |
treeCol <- .clusterMat(t(mat),
colLabel,
distance = clusteringDistanceCols,
method = clusteringMethod
)
treeCol <- clusteringCallback(treeCol, t(mat))
|
| b26d22a2 |
|
| f2a1c1ba |
mat <- mat[, treeCol$order, drop = FALSE]
fmat <- fmat[, treeCol$order, drop = FALSE]
labelsCol <- labelsCol[treeCol$order]
|
| b26d22a2 |
|
| f2a1c1ba |
if (!is.null(annotationCol) && !is.null(ncol(annotationCol))) {
annotationCol <- annotationCol[treeCol$order, , drop = FALSE]
|
| ae4c10aa |
}
|
| f2a1c1ba |
if (!is.na(cutreeCols)) {
gapsCol <- .findGaps(treeCol, cutreeCols)
|
| b26d22a2 |
} else {
|
| f2a1c1ba |
gapsCol <- NULL
|
| ae4c10aa |
}
|
| f2a1c1ba |
} else {
treeCol <- NA
treeHeightCol <- 0
}
|
| b26d22a2 |
|
| f2a1c1ba |
attr(fmat, "draw") <- fmatDraw
|
| b26d22a2 |
|
| f2a1c1ba |
# Colors and scales
if (!.is.na2(legendBreaks) & !.is.na2(legendLabels)) {
if (length(legendBreaks) != length(legendLabels)) {
stop("Lengths of legendBreaks and legendLabels must be the same")
|
| ae4c10aa |
}
|
| f2a1c1ba |
}
if (.is.na2(breaks)) {
breaks <- .generateBreaks(as.vector(mat), length(color))
}
if (legend & .is.na2(legendBreaks)) {
legend <- grid::grid.pretty(range(as.vector(breaks)))
names(legend) <- legend
}
else if (legend & !.is.na2(legendBreaks)) {
legend <- legendBreaks[legendBreaks >= min(breaks) &
legendBreaks <= max(breaks)]
if (!.is.na2(legendLabels)) {
legendLabels <- legendLabels[legendBreaks >= min(breaks) &
legendBreaks <= max(breaks)]
names(legend) <- legendLabels
} else {
names(legend) <- legend
|
| ae4c10aa |
}
|
| f2a1c1ba |
} else {
legend <- NA
}
mat <- .scaleColours(mat, col = color, breaks = breaks)
annotation <- c(annotationRow, annotationCol)
annotation <- annotation[unlist(lapply(
annotation,
function(x) !.is.na2(x)
))]
if (length(annotation) != 0) {
annotationColors <- .generateAnnotationColours(annotation,
annotationColors,
drop = dropLevels
)
} else {
annotationColors <- NA
}
labelsRow <- rownames(mat)
labelsCol <- colnames(mat)
if (!showRownames) {
labelsRow <- NULL
}
if (!showColnames) {
labelsCol <- NULL
}
# Draw heatmap
gt <- .heatmapMotor(mat,
borderColor = borderColor,
cellWidth = cellWidth,
cellHeight = cellHeight,
treeHeightCol = treeHeightCol,
treeHeightRow = treeHeightRow,
treeCol = treeCol,
treeRow = treeRow,
fileName = fileName,
width = width,
height = height,
breaks = breaks,
color = color,
legend = legend,
annotationRow = annotationRow,
annotationCol = annotationCol,
annotationColors = annotationColors,
annotationLegend = annotationLegend,
annotationNamesRow = annotationNamesRow,
annotationNamesCol = annotationNamesCol,
main = main,
fontSize = fontSize,
fontSizeRow = fontSizeRow,
fontSizeCol = fontSizeCol,
fmat = fmat,
fontSizeNumber = fontSizeNumber,
numberColor = numberColor,
gapsRow = gapsRow,
gapsCol = gapsCol,
labelsRow = labelsRow,
labelsCol = labelsCol,
...
)
|
| 1d563e1f |
return(gt)
|
| b26d22a2 |
}
|
| 916122c9 |
|
| 7ad71289 |
# order function that order the row/column labels
|
| 926f61e5 |
# based on the order of the group priority
# return value is a vector of the ordered index
# labels is a vector of any non-zero length
|
| 7ad71289 |
# groupOrder, a column named dataframe/matrix
# with the "groupName" column storing the group
|
| 926f61e5 |
# name and the "groupIndex" storing the group priority
|
| f2a1c1ba |
.Order <- function(labels, groupOrder = NULL) {
if (is.null(groupOrder)) {
return(order(labels))
} else {
# Throw error is length(unique(labels)) != nrow(groupOrder)
olabels <- plyr::mapvalues(
x = labels,
from = groupOrder[, "groupName"],
to = groupOrder[, "groupIndex"]
)
# Make sure the olabels is integer for order() function
olabels <- as.integer(olabels)
return(order(olabels))
}
|
| 916122c9 |
}
|
