I am trying to add a plot in an RMardkwon document, yet when I compile the PDF the graph is cut.
How can I adjust the size and the font family so it matches my Rmarkdown?
You can change the font size using
my_plot +
theme(text = element_text(size = 20))
Replace 20 with the desired font size.
You can change the font family using
my_plot +
theme(text = element_text(family="Times"))
Replace Times with the desired font family.
Related
I have been plotting data for years during my PhD and always had to fight with something that unfortunately plagues the scientific community: negligent data manipulation.
My problem is that when I plot with matplotlib two graphics with different number lengths in the Y axis, the result is two graphics with two different X axis sizes.
When I copy the resulting SVG image directly from Spyder IPython console (Copy SVG) and paste in Inkscape for editing, matching the axis is a painful task which requires scaling them correctly with absolute precision. I am aware there plugins that are able to rescale plots in Inkscape and etc.
Bonus solved problem 1: for some reason, the size of an SVG created by matplotlib is scaled by 0.75 relative to Inkscape
Bonus solved problem 2: Matplotlib uses... inches, so the 25.4 that is in the following code lines is simply to convert from inch to millimeters.
Sometimes, having more control at the root is better than patching and patching and patching. So here is my solution to those who have been agonizing like me over being able to have two plots with the same absolute axis sizes:
from matplotlib import pyplot as plt
inch = False # Set to True if you want to use inch (blergh...).
width = 50 # The actual size in millimeters for the X axis to have.
height = 20 # The actual size in millimeters for the Y axis to have.
figsize = [(-0.212+width)/(1+24.4*(not inch)),(-0.212+height)/(1+24.4*(not inch))] # [W, H]
# Attention to the 0.212 mm which is thickness of the axis line; the cap at the end of the axis is half of thickness and is accounted for the size of the axis in Inkscape. So, when you use the size of a line from Inkscape as the desired size of the axis in a plot from matplotlib, ax.get_linewidth() by default should be 0.8 (whatever 0.8 is.. but it seems like 0.212/25.4 * 100).
height_scale = 3 # Scale to account for the axis title, labels and ticks.
width_scale = 2 # Scale to account for the axis title, labels and ticks.
figsize = [width_scale*figsize[0]/0.75, height_scale*figsize[1]/0.75]
fig = plt.figure(figsize = (figsize[0], figsize[1]))
wpos = (50/(1+24.4*(not inch)))/(figsize[0]/0.75) # Giving 50 mm mandatory position shift for the Y axis, to accommodate the title, labels and ticks.
hpos = (40/(1+24.4*(not inch)))/(figsize[1]/0.75) # Giving 40 mm mandatory position shift for the X axis to accommodate the title, labels and ticks.
# Now comes the problem. The AXIS size is defined relatively to the FIGURE size. The following values will simply use the rescaled FIGURE sizes:
wscale = 1/width_scale # = (width_scale*figsize[0]/0.75)/width_scale = figsize[0]/0.75 which is our target size for Inkscape.
hscale = 1/height_scale
ax = fig.add_axes([wpos, hpos, wscale, hscale])
Then you can plot at will, copy the SVG output (in Spyder's IPython console, at least) and paste it in Inkscape.
The only set back is that the whole FIGURE size will be abnormal and you'll have to remove the white background from it in Inkscape. But that is something probably all of us already do.
This is a minimal working code. You can paste it in your IPython console and copy the SVG output, paste it in Inkscape and check the axis line size. It will be with a width of 50 mm and a height of 20 mm.
Using matplotlib 3.0.1, I had to make a figure where all text had to be in Open Sans Light. As the figure is quite complex, with several panels etc, I wanted to set that up using matplotlib.pyplot.rc(..) to define the default font and font weight for all elements of the figure.
The code below provides a minimal example. Because not everybody might have Open Sans installed, here I use the default font and the 'bold' weight, instead of 'light', to make it more general. So I set the default font weight, and size, then I plot a basic axis with x and y labels and some extra text.
import matplotlib.pyplot as plt
plt.style.use('default')
plt.rc('font', weight='bold', size=15)
fig, ax = plt.subplots(num=1, clear=True)
ax.set(xlabel='x-label', ylabel='y-label')
ax.text(0.2,0.4,'Text')
I expect all bits of text to be in 'bold' font weight. The tick labels and the extra bit of text are, but the x-label and y-label are not. They are in the normal weight. Screen capture here.
The x and y labels seem to get the default font name and size, but not the default weight.
As a workaround, I tried to set a default font weight in the 'axes' options, but that does not seem to be possible. "axes.labelsize" affects the font size of the x,y labels, but the font weight cannot be separately specified.
So it seems the font size is inherited by the x and y labels, if not otherwise specified through axes.labelsize, but the font weight is not inherited by the labels, nor can it be specified as a default for the axes. Note that the font name behaves yet differently. It is inherited by the x, y labels but cannot have a different default in the 'axes' option.
Is there a logic, or is that a bug?
Is there a solution to this? Or do I have to directly set the font weight onto the x-label and y-label objects?
I want the ticks in matplotlib to be typeset using Computer Modern sans-serif. How do I do this?
I would have expected this would do the trick, but it doesn't:
mpl.rcParams['font.family'] = 'computer modern sans serif'
Try this:
mpl.rcParams['font.family'] = 'sans-serif'
mpl.rcParams['font.sans-serif'] = ['computer modern']
The font.family property has five values:
'serif' (e.g., Times),
'sans-serif' (e.g., Helvetica),
'cursive' (e.g., Zapf-Chancery),
'fantasy' (e.g., Western), and
'monospace' (e.g., Courier).
After setting the font family you provide a list of fonts for matplotlib to try to find in order.
I want to use a non-standard font for labels on the axes of my matplotlib graph. I cannot assume users have installed the font, so I am providing the ttf file.
I have it working by doing the following:
fname = '/bla/bla/myfont.ttf'
ticks_font = matplotlib.font_manager.FontProperties(fname = fontPath, style='normal', size=12, weight='normal', stretch='normal')
for label in ax.get_xticklabels() :
label.set_fontproperties(ticks_font)
However, as I have many graphs with different styles, I want to move all layout to stylesheets. I've tried to do:
font.serif : '/bla/bla/myfont.ttf'
font.family :'serif'
But that doesn't seem to work.
I'm writing a script that saves a figure with multiple formatting styles among which is the font size of legend text.
The legend.labelspacing in rcparams or the matplotlibrc file specifies the label spacing in fractions of the font size, so I might expect the actual spacing to change if the font size is changed. However, since the actual spacing is probably calculated when the legend is first created, any subsequent change to the font size of existing legend text objects has no effect on the label spacing. Is there a way to update the legend label spacing after an existing legend label object's font size has been changed? In summary here's is what I would like to do:
plot something with a legend
save the figure (format according to rcparams or matplotlibrc file)
change several formatting properties (line widths, font sizes, etc.)
save the figure again with the updated formatting properties, including re-adjusted legend label spacing
Is there a way to do this without changing the rcparams and then rebuilding the figure?
Just call legend() with labelspacing parameter, here is an example:
import pylab as pl
pl.plot([0,1],[0,1], label="a")
pl.plot([0,2],[0,2], label="b")
pl.legend()
pl.savefig("p1.png")
pl.legend(labelspacing=2)
pl.savefig("p2.png")
To reuse parameters:
import pylab as pl
pl.plot([0,1],[0,1], label="a")
pl.plot([0,2],[0,2], label="b")
params = dict(loc="right", prop=dict(size=9))
pl.legend(**params)
pl.savefig("p1.png")
params["labelspacing"] = 2
pl.legend(**params)
pl.savefig("p2.png")