I have several fcontour plots, each with a colorbar. For the colorbar I'm creating extra axis. It is possible to set the position of the colorbar axis relative to their fcontour axis?
Im only able to set the position from axis relative to the figure. Thanks!
After reading the docs about mpl_toolkit.axes_grid as tcaswell suggested, I used divider = make_axes_locatable(ax) and cax = divider.append_axes("right", size="4.45%", pad=0.07,aspect = True). Usually divider.append_axes appends an axes with the same height to your plot, but as it seems you can change that setting aspect = True, and then modifying the aspect via cax.set_aspect and the size of your new axes.
The result is a colorbar which ALWAYS is beside its plot, and in my case it is a little shorter than the plot itself.
thanks tcaswell! :D
Related
I'm creating a colour map which has 64 horizontal data points and 3072 vertical. When I plot it, the scaling on both axes is the same and so the horizontal axis is super squished and tiny, and I can't get any information from it. I've tried changing the figsize parameter but nothing changes the actual plot, only the image that contains it. Any ideas on how to change my plot so that the actual length of the axes are the same? Below is my plotting code:
def plot_plot(self, data, title="Pixel Plot"):
pixel_plot = plt.imshow(data)
plt.title(title)
plt.colorbar(pixel_plot)
plt.show(pixel_plot)
thanks in advance!
I think you want the aspect option in plt.imshow().
So something like plt.imshow(data, aspect=0.1) or plt.imshow(data, aspect='equal')
See this solution: https://stackoverflow.com/a/13390798/12133280
I'm working with TraMineR and I don't know how to arrange my plot. So basically what i would like to have the legend under the plot and to remove the space between the x and y axis. Any help is welcomed.
The plot:
Sample code:
seqdplot(Activities.seq, with.legend=FALSE)
legend("bottom", legend=attr(Activities.seq, "labels"),
fill=attr(Activities.seq, "cpal"),
inset=-.1, bty="o", xpd=NA, cex=.75,ncol=3)
The family of seqplot functions offers a series of arguments to control the legend as well as the axes. Look at the help page of seqplot (and of plot.stslist.statd for specific seqdplot parameters).
For instance, you can suppress the x-axis with axes=FALSE, and the y-axis with yaxis=FALSE.
To print the legend you can let seqdplot display it automatically using the default with.legend=TRUE option and control it with for examples cex.legend for the font size, ltext for the text. You can also use the ncol argument to set the number of columns in the legend.
The seqplot functions use by default layout to organize the graphic area between the plots and the legend. If you need more fine tuning (e.g. to change the default par(mar=c(5.1,4.1,4.1,2.1)) margins around the plot and the legend), you should create separately the plot(s) and the legend and then organize them yourself using e.g. layout or par(mfrow=...). In that case, the separate graphics should be created by setting with.legend=FALSE, which prevents the display of the legend and disables the automatic use of layout.
The color legend is easiest obtained with seqlegend.
I illustrate with the mvad data that ships with TraMineR. First the default plot with the legend. Note the use of border=NA to suppress the too many vertical black lines.
library(TraMineR)
data(mvad)
mvad.scode <- c("EM", "FE", "HE", "JL", "SC", "TR")
mvad.seq <- seqdef(mvad, 17:86,
states = mvad.scode,
xtstep = 6)
# Default plot with the legend,
seqdplot(mvad.seq, border=NA)
Now, we suppress the x and y axes and modify the display of the legend
seqdplot(mvad.seq, border=NA,
axes=FALSE, yaxis=FALSE, ylab="",
cex.legend=1.3, ncol=6, legend.prop=.11)
Here is how you can control the space between the plot and the x and y axes
seqdplot(mvad.seq, border=NA, yaxis=FALSE, xaxis=FALSE, with.legend=FALSE)
axis(2, line=-1)
axis(1, line=0)
Creating the legend separately and reducing the left, top, and right margins around the legend
op <- par(mar=c(5.1,0.1,0.1,0.1))
seqlegend(mvad.seq, ncol=2, cex=2)
par(op)
I am trying to create a set of Axes.annotate() in matplotlib. I would like these annotations to be offset from the point (akin to textcoords='offset pixels') but in ‘axes fraction’ instead of absolute number of pixels.
The problem with using data coordinates, is that it gets messy when one uses logarithmic (or other) scales.
The problem with offset pixels is that the appearance changes if changing the size of the figure, or the dpi.
The following is an attempt to recapitulate the problem:
fig, axs = plt.subplots(1,2)
axs[0].plot([1,2],[10,100])
axs[1].semilogy([1,2],[10,100])
for ax in axs:
ax.annotate('', xy=(1,10), xytext=(1,50), textcoords=('data', 'offset pixels'),arrowprops={'arrowstyle':'-', 'lw':3})
plt.show()
fig, axs = plt.subplots(1,2, dpi=200)
axs[0].plot([1,2],[10,100])
axs[1].semilogy([1,2],[10,100])
for ax in axs:
ax.annotate('', xy=(1,10), xytext=(1,50), textcoords=('data', 'offset pixels'),arrowprops={'arrowstyle':'-', 'lw':3})
plt.show()
I would like to have the annotation line be the same length (relative to the size of the plots), regardless of the size of the figure, or the scaling of the axes.
Is that possible?
If you want to specify the annotation offset in units of axes fraction, just do it. The following produces the line of lentgh 20% axes fraction.
ax.annotate('', xy=(1,10), xytext=(1,0.2), textcoords=('data', 'axes fraction')
I managed to solve my problem by looking through Matplotlib's Transformation Tutorial, which already contained everything I needed.
To plot something that was of constant length relative to the axes, I used the Axes.transLimits object. But before, I have to be wary of the possibility that I'm dealing with logarithmic axes, so I'll also use the Axes.transScale object to take the (possible) non-linear scaling of the axes into account.
The code that I'm using in the end is to get the 'Axes' coordinates of my initial point, and then simply plot from that point to a certain offset from that point, specifying that my coordinates are expressed in Axes coordinate system
xax,yax = ax.transLimits.transform(ax.transScale.transform([x,y]))
ax.plot([xax,xax], [y,y+offset], transform=ax.transAxes)
I'm having trouble giving colorbars to a grid of line plots in Matplotlib.
I have a grid of plots, which each shows 64 lines. The lines depict the penalty value vs time when optimizing the same system under 64 different values of a certain hyperparameter h.
Since there are so many lines, instead of using a standard legend, I'd like to use a colorbar, and color the lines by the value of h. In other words, I'd like something that looks like this:
The above was done by adding a new axis to hold the colorbar, by calling figure.add_axes([0.95, 0.2, 0.02, 0.6]), passing in the axis position explicitly as parameters to that method. The colorbar was then created as in the example code here, by instantiating a ColorbarBase(). That's fine for single plots, but I'd like to make a grid of plots like the one above.
To do this, I tried doubling the number of subplots, and using every other subplot axis for the colorbar. Unfortunately, this led to the colorbars having the same size/shape as the plots:
Is there a way to shrink just the colorbar subplots in a grid of subplots like the 1x2 grid above?
Ideally, it'd be great if the colorbar just shared the same axis as the line plot it describes. I saw that the colorbar.colorbar() function has an ax parameter:
ax
parent axes object from which space for a new colorbar axes will be stolen.
That sounds great, except that colorbar.colorbar() requires you to pass in a imshow image, or a ContourSet, but my plot is neither an image nor a contour plot. Can I achieve the same (axis-sharing) effect using ColorbarBase?
It turns out you can have different-shaped subplots, so long as all the plots in a given row have the same height, and all the plots in a given column have the same width.
You can do this using gridspec.GridSpec, as described in this answer.
So I set the columns with line plots to be 20x wider than the columns with color bars. The code looks like:
grid_spec = gridspec.GridSpec(num_rows,
num_columns * 2,
width_ratios=[20, 1] * num_columns)
colormap_type = cm.cool
for (x_vec_list,
y_vec_list,
color_hyperparam_vec,
plot_index) in izip(x_vec_lists,
y_vec_lists,
color_hyperparam_vecs,
range(len(x_vecs))):
line_axis = plt.subplot(grid_spec[grid_index * 2])
colorbar_axis = plt.subplot(grid_spec[grid_index * 2 + 1])
colormap_normalizer = mpl.colors.Normalize(vmin=color_hyperparam_vec.min(),
vmax=color_hyperparam_vec.max())
scalar_to_color_map = mpl.cm.ScalarMappable(norm=colormap_normalizer,
cmap=colormap_type)
colorbar.ColorbarBase(colorbar_axis,
cmap=colormap_type,
norm=colormap_normalizer)
for (line_index,
x_vec,
y_vec) in zip(range(len(x_vec_list)),
x_vec_list,
y_vec_list):
hyperparam = color_hyperparam_vec[line_index]
line_color = scalar_to_color_map.to_rgba(hyperparam)
line_axis.plot(x_vec, y_vec, color=line_color, alpha=0.5)
For num_rows=1 and num_columns=1, this looks like:
I'm drawing the bloxplot shown below using python and matplotlib. Is there any way I can reduce the distance between the two boxplots on the X axis?
This is the code that I'm using to get the figure above:
import matplotlib.pyplot as plt
from matplotlib import rcParams
rcParams['ytick.direction'] = 'out'
rcParams['xtick.direction'] = 'out'
fig = plt.figure()
xlabels = ["CG", "EG"]
ax = fig.add_subplot(111)
ax.boxplot([values_cg, values_eg])
ax.set_xticks(np.arange(len(xlabels))+1)
ax.set_xticklabels(xlabels, rotation=45, ha='right')
fig.subplots_adjust(bottom=0.3)
ylabels = yticks = np.linspace(0, 20, 5)
ax.set_yticks(yticks)
ax.set_yticklabels(ylabels)
ax.tick_params(axis='x', pad=10)
ax.tick_params(axis='y', pad=10)
plt.savefig(os.path.join(output_dir, "output.pdf"))
And this is an example closer to what I'd like to get visually (although I wouldn't mind if the boxplots were even a bit closer to each other):
You can either change the aspect ratio of plot or use the widths kwarg (doc) as such:
ax.boxplot([values_cg, values_eg], widths=1)
to make the boxes wider.
Try changing the aspect ratio using
ax.set_aspect(1.5) # or some other float
The larger then number, the narrower (and taller) the plot should be:
a circle will be stretched such that the height is num times the width. aspect=1 is the same as aspect=’equal’.
http://matplotlib.org/api/axes_api.html#matplotlib.axes.Axes.set_aspect
When your code writes:
ax.set_xticks(np.arange(len(xlabels))+1)
You're putting the first box plot on 0 and the second one on 1 (event though you change the tick labels afterwards), just like in the second, "wanted" example you gave they are set on 1,2,3.
So i think an alternative solution would be to play with the xticks position and the xlim of the plot.
for example using
ax.set_xlim(-1.5,2.5)
would place them closer.
positions : array-like, optional
Sets the positions of the boxes. The ticks and limits are automatically set to match the positions. Defaults to range(1, N+1) where N is the number of boxes to be drawn.
https://matplotlib.org/3.1.1/api/_as_gen/matplotlib.pyplot.boxplot.html
This should do the job!
As #Stevie mentioned, you can use the positions kwarg (doc) to manually set the x-coordinates of the boxes:
ax.boxplot([values_cg, values_eg], positions=[1, 1.3])