Skip to main content

plotting - Preparing 2d plots for publication


When it comes to plotting a data my general attitude is to avoid post processing (say with adobe illustrator) as much as possible. To follow this strategy I would like to prepare publication-ready pdf plots with Mathematica. Here are my requirements



  • Plotted lines should have width of exactly 1pt.

  • The same should be true for the lines forming axes, frames, ticks.

  • The ticks have a commensurate length. I find it is optically pleasing to have major ticks of 4pt lengths.

  • The graph should have a dimension of one column, i.e. ~ 8.5cm or 240pt.

  • All the tick labels, axes labels, etc. should be done with 12pt Helvetica.


  • No white background.


One can argue about the art value of this setup. I, personally, find it is a good compromise between the visibility and simplicity. I remember these numbers and keep them the same across different programs and publications.


I tried to develop very easy solution that can be kept in mind. Since there is a known problem with tick length (it cannon be set explicitly) I decided to adjust the rest of parameters to this dimension. At first step I am just plotting the function


fx[x_] := 1/(Exp[-x - 7] + 1) + 1/(Exp[x - 7] + 1) - 1

with default settings and nice blue-apple color


blue = RGBColor[17.6/100, 41.6/100, 63.1/100];
u = Plot[fx[x], {x, -15, 15}, 
      PlotRange -> All, AxesLabel -> {"x", "fx(x)"}, 

      PlotStyle -> Directive[AbsoluteThickness[0.5], blue]]

The absolute thickness was set to 0.5pt because I am going to enlarge the graph on the second step:


Show[u, 
  AxesStyle -> Directive[AbsoluteThickness[0.5], 6, FontFamily -> "Helvetica"], 
  ImageSize -> 120]
Export[FileNameJoin[{$UserDocumentsDirectory, "u1.pdf"}], %]

As you see the graph has now the horizontal dimension of 120pt, i.e. 50% of the desired result. But I tolerate this since it is a vector graphics. All lines have the right thickness of 50%$\times$1pt=0.5pt and major ticks are of 50%$\times$4pt=2pt. The font sizes are also right: 50%$\times$12pt=6pt.


The only problem in present approach is wrong placement of some tick labels. Numbers -10 and 10 are vertically misaligned:



enter image description here


I would appreciate any help on this particular issue, or, on the production of publication ready graphs in general. I explicitly decline possibilities of drawing ticks manually, using additional packages or post processing. Please, feel free to criticise my artistic style.


Update


I would like to make some comments on my approach. The whole idea comes from the fact that it is unacceptable for me to use additional packages for very simple plots. At the same time I have very modest requirements on graphics parameters for visual appeal. Crucial parameters for me are the lines' thickness and the ticks' length. Since there is no simple way to set the ticks' length explicitly I am forced to rescale the image. That is, the image of 240pt is required, however, it is prepared at 120pt. Everything would be perfect provided ticks' labels are properly placed.




Comments

Post a Comment

Popular posts from this blog

plotting - Filling between two spheres in SphericalPlot3D

Manipulate[ SphericalPlot3D[{1, 2 - n}, {θ, 0, Pi}, {ϕ, 0, 1.5 Pi}, Mesh -> None, PlotPoints -> 15, PlotRange -> {-2.2, 2.2}], {n, 0, 1}] I cant' seem to be able to make a filling between two spheres. I've already tried the obvious Filling -> {1 -> {2}} but Mathematica doesn't seem to like that option. Is there any easy way around this or ... Answer There is no built-in filling in SphericalPlot3D . One option is to use ParametricPlot3D to draw the surfaces between the two shells: Manipulate[ Show[SphericalPlot3D[{1, 2 - n}, {θ, 0, Pi}, {ϕ, 0, 1.5 Pi}, PlotPoints -> 15, PlotRange -> {-2.2, 2.2}], ParametricPlot3D[{ r {Sin[t] Cos[1.5 Pi], Sin[t] Sin[1.5 Pi], Cos[t]}, r {Sin[t] Cos[0 Pi], Sin[t] Sin[0 Pi], Cos[t]}}, {r, 1, 2 - n}, {t, 0, Pi}, PlotStyle -> Yellow, Mesh -> {2, 15}]], {n, 0, 1}]
Post a Comment
Read more

plotting - Plot 4D data with color as 4th dimension

I have a list of 4D data (x position, y position, amplitude, wavelength). I want to plot x, y, and amplitude on a 3D plot and have the color of the points correspond to the wavelength. I have seen many examples using functions to define color but my wavelength cannot be expressed by an analytic function. Is there a simple way to do this? Answer Here a another possible way to visualize 4D data: data = Flatten[Table[{x, y, x^2 + y^2, Sin[x - y]}, {x, -Pi, Pi,Pi/10}, {y,-Pi,Pi, Pi/10}], 1]; You can use the function Point along with VertexColors . Now the points are places using the first three elements and the color is determined by the fourth. In this case I used Hue, but you can use whatever you prefer. Graphics3D[ Point[data[[All, 1 ;; 3]], VertexColors -> Hue /@ data[[All, 4]]], Axes -> True, BoxRatios -> {1, 1, 1/GoldenRatio}]
Post a Comment
Read more

plotting - Mathematica: 3D plot based on combined 2D graphs

I have several sigmoidal fits to 3 different datasets, with mean fit predictions plus the 95% confidence limits (not symmetrical around the mean) and the actual data. I would now like to show these different 2D plots projected in 3D as in but then using proper perspective. In the link here they give some solutions to combine the plots using isometric perspective, but I would like to use proper 3 point perspective. Any thoughts? Also any way to show the mean points per time point for each series plus or minus the standard error on the mean would be cool too, either using points+vertical bars, or using spheres plus tubes. Below are some test data and the fit function I am using. Note that I am working on a logit(proportion) scale and that the final vertical scale is Log10(percentage). (* some test data *) data = Table[Null, {i, 4}]; data[[1]] = {{1, -5.8}, {2, -5.4}, {3, -0.8}, {4, -0.2}, {5, 4.6}, {1, -6.4}, {2, -5.6}, {3, -0.7}, {4, 0.04}, {5, 1.0}, {1, -6.8}, {2, -4.7}, {3, -1.
Post a Comment
Read more