New boxplot features

new_boxplot_method.py

    def boxplot(self, x, notch=0, sym='+', vert=1, whis=1.5,
                positions=None, widths=None, means=0, fill=0,
                linestyle='-', monochrome=0, limits=None,
                notchsize=None):
        """
        boxplot(x, notch=0, sym='+', vert=1, whis=1.5,
                positions=None, widths=None, means=0, fill=0,
                linestyle='-', monochrome=0, limits=None,
                notchsize=None)

        Make a box and whisker plot for each column of x or
        each vector in sequence x.
        The box extends from the lower to upper quartile values
        of the data, with a line at the median.  The whiskers
        extend from the box to show the range of the data.  Flier
        points are those past the end of the whiskers.

        notch = 0 (default) produces a rectangular box plot.
        notch = 1 will produce a notched box plot.
        notch = 2 will additionally keep the notch size constant,
        replacing the box altogether with a notch if the box
        becomes smaller than the box limits.

        sym (default '+') is the default symbol for flier points.
        Enter an empty string ('') if you don't want to show fliers.

        vert = 1 (default) makes the boxes vertical.
        vert = 0 makes horizontal boxes.  This seems goofy, but
        that's how Matlab did it.

        whis (default 1.5) defines the length of the whiskers as
        a function of the inner quartile range.  They extend to the
        most extreme data point within ( whis*(75%-25%) ) data range.

        positions (default 1,2,...,n) sets the horizontal positions of
        the boxes. The ticks and limits are automatically set to match
        the positions.

        widths is either a scalar or a vector and sets the width of
        each box. The default is 0.5, or 0.15*(distance between extreme
        positions) if that is smaller.

        means = 0 (default) does not indicate the mean of the data.
        means = 1 plots a dashed black line in the box indicating
        the mean of the data.

        fill = 1 fills the box in white
        fill = 0 (default) leaves the box open

        linestyle sets the line style of the whiskers.

        monochrome = 0 (default) uses color in the plot.
        monochrome = 1 uses a monochrome color scheme.

        limits sets the axis limits for the plot (default = None for
        automatic setting)

        notchsize = None (default) -- unused unless notch == 2
        notchsize fixes a notch to be a constant size when notch == 2

        x is an array or a sequence of vectors.

        Returns a dict of the lines added, keyed by 'boxes', 'caps',
        'whiskers', 'medians', 'fliers', and 'means'.

        """
        if not self._hold: self.cla()
        holdStatus = self._hold
        whiskers, caps, boxes, medians, fliers, means = [], [], [], [], [], []

        # convert x to a list of vectors
        if hasattr(x, 'shape'):
            if len(x.shape) == 1:
                if hasattr(x[0], 'shape'):
                    x = list(x)
                else:
                    x = [x,]
            elif len(x.shape) == 2:
                nr, nc = x.shape
                if nr == 1:
                    x = [x]
                elif nc == 1:
                    x = [ravel(x)]
                else:
                    x = [x[:,i] for i in range(nc)]
            else:
                raise ValueError, "input x can have no more than 2 dimensions"
        if not hasattr(x[0], '__len__'):
            x = [x]
        col = len(x)

        # get some plot info
        if positions is None:
            positions = range(1, col + 1)
        if widths is None:
            distance = max(positions) - min(positions)
            widths = min(0.15*max(distance,1.0), 0.5)
        if isinstance(widths, float) or isinstance(widths, int):
            widths = ones((col,), 'd') * widths

        # loop through columns, adding each to plot
        self.hold(True)
        for i,pos in enumerate(positions):
            d = ravel(x[i])
            row = len(d)
            # get mean
            mean = sum(d)/len(d)
            # get median and quartiles
            q1, med, q3 = prctile(d,[25,50,75])
            # get high extreme
            iq = q3 - q1
            hi_val = q3 + whis*iq
            wisk_hi = compress( d <= hi_val , d )
            if len(wisk_hi) == 0:
                wisk_hi = q3
            else:
                wisk_hi = max(wisk_hi)
            # get low extreme
            lo_val = q1 - whis*iq
            wisk_lo = compress( d >= lo_val, d )
            if len(wisk_lo) == 0:
                wisk_lo = q1
            else:
                wisk_lo = min(wisk_lo)
            # get fliers - if we are showing them
            flier_hi = []
            flier_lo = []
            flier_hi_x = []
            flier_lo_x = []
            if len(sym) != 0:
                flier_hi = compress( d > wisk_hi, d )
                flier_lo = compress( d < wisk_lo, d )
                flier_hi_x = ones(flier_hi.shape[0]) * pos
                flier_lo_x = ones(flier_lo.shape[0]) * pos

            # get x locations for fliers, whisker, whisker cap and box sides
            box_x_min = pos - widths[i] * 0.5
            box_x_max = pos + widths[i] * 0.5

            wisk_x = ones(2) * pos

            cap_x_min = pos - widths[i] * 0.25
            cap_x_max = pos + widths[i] * 0.25
            cap_x = [cap_x_min, cap_x_max]

            # get y location for median, mean
            med_y = [med, med]
            mean_y = [mean, mean]

            # calculate 'regular' plot
            no_box = False
            if notch == 0:
                # make our box vectors
                box_x = [box_x_min, box_x_max, box_x_max, box_x_min, box_x_min]
                box_y = [q1, q1, q3, q3, q1 ]
                # make our median, mean line vectors
                med_x = [box_x_min, box_x_max]
                mean_x = [box_x_min, box_x_max]
            # calculate 'notch' plot
            else:
                if notch == 1:
                    notch_max = med + 1.57*iq/sqrt(row)
                    notch_min = med - 1.57*iq/sqrt(row)
                    if notch_max > q3:
                        notch_max = q3
                    if notch_min < q1:
                        notch_min = q1
                else:
                    if notchsize is None:
                        raise ValueError("Must supply notchsize when notch==2")
                    notch_max = med + notchsize
                    notch_min = med - notchsize
                    # force 'no box' if notch size outside of box limits
                    if notch_max > q3 or notch_min < q1:
                        no_box = True

                # make our notched box vectors
                if no_box:
                    box_x = [box_x_max, cap_x_max, box_x_max]
                    notch2_x = [box_x_min, cap_x_min, box_x_min]
                    box_y = [notch_min, med, notch_max]
                    notch2_y = [notch_max, med, notch_min]
                else:
                    box_x = [box_x_min, box_x_max, box_x_max, cap_x_max, box_x_max, box_x_max, box_x_min, box_x_min, cap_x_min, box_x_min, box_x_min]
                    box_y = [q1, q1, notch_min, med, notch_max, q3, q3, notch_max, med, notch_min, q1]
                # make our median, mean line vectors
                med_x = [cap_x_min, cap_x_max]
                mean_x = [box_x_min, box_x_max]   # doesn't take into account notch shape

            if monochrome:
                wiskcol = capcol = boxcol = medcol = symcol = 'k'
            else:
                wiskcol, capcol, boxcol, medcol, symcol = 'b', 'k', 'b', 'r', 'b'

            if fill and not no_box:
                self.fill(box_x, box_y, facecolor='w')

            # vertical or horizontal plot?
            if vert:
                def doplot(*args):
                    return self.plot(*args)
            else:
                def doplot(*args):
                    shuffled = []
                    for i in range(0, len(args), 3):
                        shuffled.extend([args[i+1], args[i], args[i+2]])
                    return self.plot(*shuffled)

            whiskers.extend(doplot(wisk_x, [q1, wisk_lo], wiskcol+linestyle,
                                   wisk_x, [q3, wisk_hi], wiskcol+linestyle))
            caps.extend(doplot(cap_x, [wisk_hi, wisk_hi], capcol+'-',
                               cap_x, [wisk_lo, wisk_lo], capcol+'-'))
            boxes.extend(doplot(box_x, box_y, boxcol+'-'))
            medians.extend(doplot(med_x, med_y, medcol+'-'))
            fliers.extend(doplot(flier_hi_x, flier_hi, symcol+sym,
                                 flier_lo_x, flier_lo, symcol+sym))
            if means:
                if notch > 0:
                    nstyle = 'k-'
                else:
                    nstyle = 'k:'
                means.extend(doplot(mean_x, mean_y, nstyle))
            if notch == 2 and no_box:
                boxes.extend(doplot(notch2_x, notch2_y, boxcol+'-'))

        # fix our axes/ticks up a little
        if 1 == vert:
            setticks, setlim = self.set_xticks, self.set_xlim
        else:
            setticks, setlim = self.set_yticks, self.set_ylim

        # use explicit axis limits if provided
        if limits is None:
            newlimits = min(positions)-0.5, max(positions)+0.5
            setlim(newlimits)
            setticks(positions)
        elif limits != ():
            setlim(limits)
            setticks([])

        # reset hold status
        self.hold(holdStatus)

        return dict(whiskers=whiskers, caps=caps, boxes=boxes,
                    medians=medians, fliers=fliers, means=means)