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qscatter.R
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qscatter.R
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#' Draw a scatter plot
#'
#' This function creates a scatter plot with two numeric variables. It supports
#' colors and sizes generated by \code{\link{qdata}}. When the sizes are not the
#' same, a scatter plot becomes what is called the ``bubble chart''.
#'
#' All the common interactions like brushing and deleting are documented in
#' \code{\link{common_key_press}}.
#'
#' In the identify mode, the plot will show the row id(s) of the identified
#' point(s) as well as \code{x} and \code{y} values.
#'
#' Arrow keys are used in scatter plots for interactions: without the
#' \code{Shift} key, \code{Up} and \code{Down} will increase/decrease the sizes
#' of points; with the \code{Shift} key being pressed, \code{Up}, \code{Down},
#' \code{Left} and \code{Right} will move the (background of) plot to the
#' corresponding direction.
#'
#' Mouse wheel is used to zoom in and zoom out the plot. Together with keyboard
#' interactions, this will enable us to see details in data.
#' @param x the name of the x variable
#' @param y the name of the y variable (if missing, \code{x} will be plotted
#' against its indices, i.e., \code{y} will become \code{x} and \code{x} will
#' be indices)
#' @inheritParams qbar
#' @param asp aspect ratio (ratio of the physical height of a plot to its width;
#' unlike other R graphics systems, this will \emph{not} affect the ranges of
#' axes)
#' @return A scatter plot
#' @author Heike Hofmann, Di Cook, Yihui Xie
#' @note Using more than one color (including border colors) can lead to serious
#' speed issues; this plot is fastest when we only use a single color and a
#' single size. As the number of unique colors increases, the plotting can be
#' slower based on a same dataset. Using more than one size is also slower
#' than using a single size for all points; the internal painting functions
#' are different for the two cases (\code{\link[qtpaint]{qdrawCircle}} for the
#' former, and \code{\link[qtpaint]{qdrawGlyph}} for the latter).
#' @export
#' @example inst/examples/qscatter-ex.R
qscatter = function(x, y, data, main = '', xlim = NULL, ylim = NULL,
xlab = NULL, ylab = NULL, asp = 1, alpha = 1, unibrushcolor = TRUE) {
data = check_data(data)
b = brush(data)
z = as.list(match.call()[-1])
## initialize meta
meta = Scat.meta$new(xvar = as.character(z$x), yvar = as.character(z$y),
xy = matrix(nrow = nrow(data), ncol = 2), active = TRUE,
alpha = alpha, main = main, asp = asp, minor = 'xy',
samesize = diff(range(data$.size, na.rm=TRUE, finite=TRUE)) < 1e-7)
## set default xlab/ylab if not provided
if (is.null(xlab)) meta$xlab = meta$xvar
if (is.null(ylab)) meta$ylab = meta$yvar
if (!(meta$xvar %in% names(data))) meta$xvar = x
if (!(meta$yvar %in% names(data))) meta$yvar = y
## tour: color, size, transparency could be decided by proj3
if ('proj3' %in% colnames(data)) {
if (which(colnames(data) == 'proj3')[1] > which(colnames(data) == '.border')) {
dim3 = c('proj1','proj2','proj3')
meta$dim3 = dim3[! (dim3 %in% c(meta$xvar, meta$yvar))][1]
}
} else meta$dim3 = NULL
## reorder the points according to color/border for drawing speed
compute_order = function() {
meta$order = if (!is.null(meta$dim3)) {
order(data[,meta$dim3], decreasing=TRUE)
} else {
order(data$.color, data$.border) # the ideal order to draw
}
}
compute_order()
update_limits = function(r) {
# r is new range of limits - 2 by 2 matrix
meta$limits = r
meta$xlabels = format(meta$xat <- axis_loc(r[, 1]))
meta$ylabels = format(meta$yat <- axis_loc(r[, 2]))
meta$xlab = if (is.null(xlab)) meta$xvar else xlab
meta$ylab = if (is.null(ylab)) meta$yvar else ylab
}
## compute coordinates/axes-related stuff
compute_coords = function() {
if (is.null(z$y)) {
meta$yvar = meta$xvar # when y is missing, make it x
meta$xvar = 'index'
meta$xy[, 1] = seq(sum(idx))
} else {
meta$xy[, 1] = data[, meta$xvar]
}
meta$xy[, 2] = data[, meta$yvar]
idx = visible(data)[meta$order]
x = meta$xy[idx, 1]; meta$xlim = range(x, na.rm = TRUE, finite = TRUE)
y = meta$xy[idx, 2]; meta$ylim = range(y, na.rm = TRUE, finite = TRUE)
r = cbind(if (is.null(xlim)) meta$xlim else xlim,
if (is.null(ylim)) meta$ylim else ylim)
update_limits(extend_ranges(r))
}
compute_coords()
## aesthetics (colors)
compute_aes = function() {
ord = meta$order; idx = visible(data)[ord] # reorder aesthetics according to vis
meta$color = data$.color[ord][idx]; meta$border = data$.border[ord][idx]
meta$size = data$.size[ord][idx]
if (!is.null(meta$dim3)) {
dim3scale=(1-rescaler(data[ord,meta$dim3][idx],type='range'))*0.66+0.33
meta$color = alpha(meta$color, dim3scale)
meta$border = alpha(meta$border, dim3scale)
meta$size = meta$size * dim3scale
}
if (length(unique(meta$color)) == 1) meta$color = meta$color[1]
if (length(unique(meta$border)) == 1) meta$border = meta$border[1]
if (meta$samesize) meta$size = meta$size[1]
}
compute_aes()
## initialize brush size (1/15 of the layer size)
meta$brush.size = c(1, -1) * apply(meta$limits, 2, diff) / 15
b$alpha = alpha
## colorful brush setting
if (!unibrushcolor) {
meta$current_color = data$.color
meta$current_border = data$.border
}
## draw points
main_draw = function(layer, painter) {
ord = meta$order; idx = visible(data)[ord]
stroke = meta$border
fill = meta$color
if (meta$alpha < 1) {
# adjust colors
stroke = alpha(stroke, meta$alpha); fill = alpha(fill, meta$alpha)
}
if (meta$samesize) {
qdrawGlyph(painter, qglyphCircle(r = meta$size),
meta$xy[ord, 1][idx], meta$xy[ord, 2][idx],
stroke = stroke, fill = fill)
} else {
qdrawCircle(painter, meta$xy[ord, 1][idx], meta$xy[ord, 2][idx], r = meta$size,
stroke = stroke, fill = fill)
}
if (!is.null(bd <- bound_seg(meta)))
qdrawSegment(painter, bd[, 1], bd[, 2], bd[, 3], bd[, 4], stroke = "red")
meta$brush.adj = one_pixel(painter) * min(meta$size)
}
## draw brushed points
brush_draw = function(layer, painter) {
idx = selected(data)
if (any(idx)) {
if (unibrushcolor) {
fill_color = b$color
} else { # colorful brush
idx = which(idx)[order(meta$current_color[idx])]
if (any(data$.color==meta$current_color)) {
data$.color = alpha(meta$current_color, 0.1)
data$.border = alpha(meta$current_border, 0.1)
}
fill_color = meta$current_color[idx]
}
fill_color = alpha(fill_color, b$alpha)
if (meta$samesize) {
qdrawGlyph(painter, qglyphCircle(r = sqrt(b$size) * meta$size),
meta$xy[idx, 1], meta$xy[idx, 2],
stroke = fill_color, fill = fill_color)
} else {
qdrawCircle(painter, meta$xy[idx, 1], meta$xy[idx, 2],
r = sqrt(b$size) * data$.size[idx],
stroke = fill_color, fill = fill_color)
}
} else {
if (!unibrushcolor){
data$.color = meta$current_color
data$.border = meta$current_border
}
}
draw_brush(layer, painter, data, meta)
}
## events
brush_mouse_press = function(layer, event) {
common_mouse_press(layer, event, data, meta)
}
tree = createTree(meta$xy) # build a search tree
brush_mouse_move = function(layer, event) {
rect = update_brush_size(meta, event)
rect[1, ] = rect[1, ] - meta$brush.adj
rect[2, ] = rect[2, ] + meta$brush.adj
if (!(b$select.only && b$draw.brush)) {
hits = rectLookup(tree, rect[1, ], rect[2, ])
selected(data) = mode_selection(selected(data), hits, mode = b$mode)
} else qupdate(layer.brush)
common_mouse_move(layer, event, data, meta)
}
brush_mouse_release = function(layer, event) {
common_mouse_release(layer, event, data, meta)
brush_mouse_move(layer, event)
}
key_press = function(layer, event) {
common_key_press(layer, event, data, meta)
if (!unibrushcolor) {
meta$current_color = data$.color # colorful brush
meta$current_border = data$.border
}
shift = event$modifiers() == Qt$Qt$ShiftModifier
if (shift && length(i <- which(match_key(c('Left', 'Right', 'Up', 'Down'))))) {
j = c(1, 1, 2, 2)[i]; k = c(1, -1, -1, 1)[i]
meta$limits[, j] = extend_ranges(meta$limits[, j], k * c(1, -1) * 0.02)
update_limits(meta$limits)
} else if (length(i <- which(match_key(c('Up', 'Down'))))) {
## change size
data$.size = pmax(0.1, c(1.1, 0.9)[i] * data$.size)
}
}
key_release = function(layer, event) {
common_key_release(layer, event, data, meta)
}
mouse_wheel = function(layer, event) {
pos = as.numeric(event$pos())
lim = meta$limits
p = (pos - lim[1, ]) / (lim[2, ] - lim[1, ]) # proportions to left/bottom
update_limits(extend_ranges(meta$limits,
-sign(event$delta()) * 0.1 * c(p[1], 1 - p[1], p[2], 1 - p[2])))
}
identify_hover = function(layer, event) {
if (!b$identify) return()
b$cursor = 2L
meta$pos = as.numeric(event$pos())
rect = as.matrix(identify_rect(meta))
meta$identified = rectLookup(tree, rect[1, ], rect[2, ])
qupdate(layer.identify)
}
identify_draw = function(layer, painter) {
if (!b$identify || !length(idx <- meta$identified)) return()
meta$identify.labels = sprintf(
'row id: %s\n%s: %s\n%s: %s',
paste(rownames(data)[idx], collapse = ', '),
meta$xvar, paste(meta$xy[idx, 1], collapse = ', '),
meta$yvar, paste(meta$xy[idx, 2], collapse = ', ')
)
draw_identify(layer, painter, data, meta)
if (meta$samesize) {
qdrawGlyph(painter, qglyphCircle(r = 2 * sqrt(b$size) * meta$size),
meta$xy[idx, 1], meta$xy[idx, 2], stroke = b$color, fill = NA)
} else {
qdrawCircle(painter, meta$xy[idx, 1], meta[idx, 2],
r = sqrt(b$size) * data$.size[idx], stroke = b$color, fill = NA)
}
}
## create layers
scene = qscene()
scene$setItemIndexMethod(Qt$QGraphicsScene$NoIndex)
layer.root = qlayer(scene)
layer.main = qlayer(
paintFun = main_draw,
mousePressFun = brush_mouse_press, mouseReleaseFun = brush_mouse_release,
mouseMove = brush_mouse_move, hoverMoveFun = identify_hover,
keyPressFun = key_press, keyReleaseFun = key_release,
wheelFun = mouse_wheel,
focusInFun = function(layer, event) {
common_focus_in(layer, event, data, meta)
}, focusOutFun = function(layer, event) {
common_focus_out(layer, event, data, meta)
},
limits = qrect(meta$limits), clip = TRUE, cache = .cache())
layer.brush = qlayer(paintFun = brush_draw, limits = qrect(meta$limits))
layer.identify = qlayer(paintFun = identify_draw, limits = qrect(meta$limits))
layer.title = qmtext(meta = meta, side = 3, cache = .cache())
layer.xlab = qmtext(meta = meta, side = 1, cache = .cache())
layer.ylab = qmtext(meta = meta, side = 2, cache = .cache())
layer.xaxis = qaxis(meta = meta, side = 1, cache = .cache())
layer.yaxis = qaxis(meta = meta, side = 2, cache = .cache())
layer.grid = qgrid(meta = meta, cache = TRUE)
layer.root[0, 2] = layer.title
layer.root[2, 2] = layer.xaxis
layer.root[3, 2] = layer.xlab
layer.root[1, 1] = layer.yaxis
layer.root[1, 0] = layer.ylab
layer.root[1, 2] = layer.grid
layer.root[1, 2] = layer.main
layer.root[1, 2] = layer.brush
layer.root[1, 2] = layer.identify
layer.root[1, 3] = qlayer()
## set sizes of layers (arrange the layout)
set_layout = function() {
fix_dimension(layer.root,
row = list(id = c(0, 2, 3), value = c(prefer_height(meta$main),
prefer_height(meta$xlabels),
prefer_height(meta$xlab))),
column = list(id = c(1, 0, 3), value = c(prefer_width(meta$ylabels),
prefer_width(meta$ylab, FALSE),
10)))
}
set_layout()
## layout is dynamic (listen to changes in xlab/ylab/xlabels/ylabels...)
meta$mainChanged$connect(set_layout)
meta$xlabChanged$connect(set_layout); meta$ylabChanged$connect(set_layout)
meta$xlabelsChanged$connect(set_layout); meta$ylabelsChanged$connect(set_layout)
## finally create the view and set window title
view = qplotView(scene = scene)
view$setWindowTitle(paste("Scatterplot:", meta$xvar, meta$yvar))
meta$xvarChanged$connect(function() {
view$setWindowTitle(paste("Scatterplot:", meta$xvar, meta$yvar))
})
if (!is.null(asp)) view$resize(480, 480 * asp) # aspect ratio
## listeners on the data (which column updates which layer(s))
d.idx = add_listener(data, function(i, j) {
idx = which(j == c(meta$xvar, meta$yvar, '.brushed', '.visible', '.color', '.border'))
if (length(idx) < 1) {
compute_coords(); compute_aes()
meta$samesize = diff(range(data$.size, na.rm = TRUE, finite = TRUE)) < 1e-7
qupdate(layer.grid); qupdate(layer.xaxis); qupdate(layer.yaxis)
qupdate(layer.main)
return()
} else idx = c(1, 1, 2, 3, 4, 4)[idx]
switch(idx, {
# update at least one of the axes
compute_coords();
# maybe check whether tour is on and not change tree in that case ...
tree <<- createTree(meta$xy)
}, qupdate(layer.brush), {
compute_coords(); selected(data)[!visible(data)] = FALSE
}, {
compute_order(); compute_aes(); qupdate(layer.main)
})
})
## when layer is destroyed, remove the listener from data
qconnect(layer.main, 'destroyed', function(x) {
## b$colorChanged$disconnect(b.idx)
remove_listener(data, d.idx)
})
## when b$cursor is changed, update cursor on screen
b$cursorChanged$connect(function() {
set_cursor(view, b$cursor)
})
## these layers have the same limits from meta$limits
sync_limits(meta, layer.main, layer.brush, layer.identify)
## simulate brushing
meta$manual.brush = function(pos) {
brush_mouse_move(layer = layer.main, event = list(pos = function() pos))
}
## attach meta to the returned value (for post-processing or debugging)
attr(view, 'meta') = meta
view
}
Scat.meta = setRefClass("Scat_meta",
fields = properties(c(
Common.meta,
list(xvar = 'character', yvar = 'character', order = 'numeric',
xy = 'matrix', asp = 'numeric', samesize = 'logical')
)))
## order is for keeping track of the original order of data