I am new to gnuplot. I am trying to superimpose both a contour plot and some data points on the x-y plane.
Data for my contour is given (surface1.txt) here
Data for the single points is given (points1.txt) here
I am trying to run this script:
set multiplot
# plot the contour from the surface1.txt
unset key
set dgrid3d
unset surface
set contour base
# these values need to be set (requirement)
set cntrparam level incremental 0.16, 0.259, 4.47
set view 0,0
unset ztics
splot "surface1.txt" with lines
# plot the points on the x-y plane
unset xtics
unset ytics
splot "points1.txt"
unset multiplot
and I am getting this output:
As you can see, the single points that I am trying to put on the x-y plane also comes as contour, what I need to do is:
display the points from "points1.txt" as single points (not contour)
the plot is zoomed out, I need a full screen image.
move the y-axis ticks from right to left vertical.
remove all the colors. I need a grayscale image.
Please help.
EDIT:
I have also tried this way --
set contour base
set cntrparam bspline
set cntrparam level incremental 0.16, 0.259, 4.47
set view map
set dgrid3d
unset key
splot 'surface1.txt' nosurface with lines, \
'points1.txt' nocontour
and I am getting this plot --
There are several things you must regard:
set dgrid3d interpolates your data and is thought to be used for non-gridded data. There is no option nodgrid3d which allows you to use it only for one plot part. This is what you see in your second attempt: the data for the points is interpolated and a 10x10 grid is generated.
However, you don't need to use this, because you have gridded data, but are missing a few empty lines in your data file. Just insert a single empty line when the x-value changes, like:
...
0.0 0.7999999999999999 2.0477812692428836
0.0 0.8999999999999999 2.3096674656635523
0.0 0.9999999999999999 2.5772908911794614
0.1 0.0 0.8254201558219569
0.1 0.1 1.0350909705482707
0.1 0.2 1.2504990143698247
...
Use the nosurface option for the contours, and nocontours when plotting the points.
A possible script could be:
set contour base
set cntrparam level incremental 0.16, 0.259, 4.47
unset key
set view map
set for [i=1:20] linetype i lc rgb 'black'
set terminal pngcairo dashed size 600,400
set output 'contour-with-points.png'
splot 'surface1.txt' with lines nosurface, 'points1.txt' with points nocontour pt 7
with the result
I used the pngcairo terminal only for this example, for your document you should probably use a vector format, like produced by pdfcairo, postscript, epslatex or similar.
Related
I have a simple data I want to plot as 3D plot (3 columns divided by a comma):
33.26,0.0000001,1
67.02,0.0000010,2
101.64,0.0000100,3
137.53,0.0001000,4
175.06,0.0010000,5
214.59,0.0100000,6
256.47,0.1000000,7
301.09,1.0000000,8
348.78,10.0000000,9
399.92,100.0000000,10
454.87,1000.0000000,11
513.99,10000.0000000,12
577.65,10000.0000000,13
646.22,10000.0000000,14
720.05,10000.0000000,15
799.51,10000.0000000,16
884.96,10000.0000000,17
976.77,10000.0000000,18
1075.29,10000.0000000,19
1180.89,10000.0000000,20
1293.92,10000.0000000,21
1414.77,10000.0000000,22
1431.83,10000.0000000,23
1449.15,10000.0000000,24
1466.97,10000.0000000,25
1485.79,10000.0000000,26
1505.97,10000.0000000,27
1527.88,10000.0000000,28
1551.87,10000.0000000,29
1578.3,10000.0000000,30
1607.56,10000.0000000,31
1639.98,10000.0000000,32
1675.95,10000.0000000,33
1715.82,10000.0000000,34
1759.96,10000.0000000,35
1808.72,10000.0000000,36
1862.49,10000.0000000,37
1921.6,10000.0000000,38
1986.44,10000.0000000,39
2057.35,10000.0000000,40
2134.71,10000.0000000,41
2218.87,10000.0000000,42
2310.2,10000.0000000,43
2409.06,10000.0000000,44
2515.83,10000.0000000,45
I wrote a simple script to plot the above data:
#!/usr/bin/gnuplot
set palette rgbformulae 33,13,10
set datafile separator ","
set terminal postscript eps size 10.5, 5.62 enhanced color font 'Helvetica,20' linewidth 2
set output 'test.eps'
set xlabel "time [s] (no operation)" offset -4, 0, 0
set xtics left offset 0,-0.3 rotate by 45 right
set xrange [0:400]
set ylabel "ranges" offset 2, 0, 0
set ytics left offset 0,-0.5
set zlabel "devices" offset -4, 0, 0
set zrange [0:50]
set autoscale
set title " "
set key inside left top;
set dgrid3d 30,30
set hidden3d
set style line 1 linecolor rgb '00FF00' linetype 4 linewidth 1
splot "data.csv" u 1:2:3 title "" with lines palette
And my output:
As you all can see, the output image (or, I should say), the x,y and z ticks on axis x,y, and z are not enough detailed. It is hard to say that the output image was plotted with this data.
Is there a way that would let me manipulate the x,y, and z ticks, to be taken from file, in some elegant way?
I also would like the image to be more readable with new x,y, and z ticks, so I think that the 10000.0000000 value should appear only once, when it appeared for the first time in data file.
Thank you.
Not exactly an answer to your question, and it is my personal opinion, but you might be interested in the ideas:
The data seems not to be grid data, so I would not use a surface plot of any kind.
Plotting only the datapoints in 3d does not give a useful picture, it is only a single line somewhere in space. I would try to use a 2D plot which contains the height information as color.
I would use a logscale for the y-axis.
This leads to the following script:
set terminal pngcairo
set output 'test.png'
set datafile separator ","
set palette rgbformulae 33,13,10
# Set margins to keep colorbox label inside the picture
set lmargin screen 0.12
set rmargin screen 0.85
set xlabel "time [s] (no operation)"
set ylabel "ranges"
set cblabel "devices"
unset key
set yrange [1e-8:1e5]
set ytics format "1e%+T"
set logscale y
set view map
set cbrange [0:50]
set zrange [0:50]
splot "data.csv" u 1:2:3 w p pt 7 palette ,\
"data.csv" every 5::4 u ($1+0):($2/3):(0):($3 != 30 ? 3 : "") with labels
It also prints the z-labels of some datapoints, skipping 30 for spacing reasons.
This is the result:
i am 3d plotting a matrix with some values, and i need to add contour lines to the plot, is there a simple gnuplot command to do this?
I tried the command: "set contour base" but only 1 line came up, i think it should be many lines. See matlab picture
When i plot it in gnuplot i only get 1 contour line in the top left corner.But everything else is correct.
My goal is to get it to look like in matlab like this Matlabplot
I also found this example: see link in comments (dont have enough rep), but i dont understand where i should put in the data values from test.txt
test.txt
test.txt
gnuplot commands
set view map
set yrange [0:30]
set xrange [0:30]
set dgrid3d 100,100,4
set contour base
splot 'test.txt' u 1:2:3 w pm3d
What you are missing is to tell gnuplot where to put the contours. This is done via the set cntrparam levels incr -0.3,0.1,0.5 command which means: start at -0.3 and trace a contour every o.1 up to 0.5.
AFAIK if you want to make contours all black, you have to save the contour lines in a temporary file (here contour.txt).
So your script would be
reset
set contour
unset surface
set cntrparam levels incr -0.3,0.1,0.5
set view map
set xrange [0:30]
set yrange [0:30]
set dgrid3d 100,100,4
set table "contour.txt"
splot 'test.txt'
unset table
unset contour
set surface
set table "dgrid.txt"
splot 'test.txt'
unset table
reset
set pm3d map
unset key
set palette defined (0 '#352a87', 1 '#0363e1',2 '#1485d4', 3 '#06a7c6', 4 '#38b99e', 5 '#92bf73', 6 '#d9ba56', 7 '#fcce2e', 8 '#f9fb0e')
set autoscale fix
set grid
splot 'dgrid.txt' w pm3d, 'contour.txt' w l lc rgb "black"
which gives you this:
Note:
you can get rid of interpolation file (dgrid.txt) if you format a bit your datafile by leaving a blank line after each row (i.e. every 30 datapoints) because they are already mesh-ordered.
This could be done also with a awk script. But I'm too lazy to look into it...
The rest will remain the same and will work as expected.
here is how it should look like :
In which case the script would simply become:
set pm3d map impl
set contour
set style increment user
do for [i=1:18] { set style line i lc rgb "black"}
set cntrparam levels incr -0.3,0.1,0.5
set palette defined (0 '#352a87', 1 '#0363e1',2 '#1485d4', 3 '#06a7c6', 4 '#38b99e', 5 '#92bf73', 6 '#d9ba56', 7 '#fcce2e', 8 '#f9fb0e')
set autoscale fix
splot 'test.txt' w pm3d notitle
with no need of ntermediate file and with better contour since data in not interpolate by gridded:
I have an infrared spectrum for a compound of interest that I would like to plot, and I have a spectrum.dat file with all of the data points. It is of the form:
# X Y
300 100
301 100
302 99
303 70
...
3999 98
4000 100
I would like to plot this using an x axis typical of IR spectra, but I am having trouble doing so. If you are unfamiliar, this is what a typical IR spectrum might look like (aside from the labels on the graph itself). Notice that the x-axis is reversed, and that it abruptly doubles its scaling above 2000 units (reciprocal centimeters). Is there a way to coerce Gnuplot into plotting my data this way? I so far have managed to come up with the following script:
# Make an SVG of size 800x500
set terminal svg size 800,500 fname 'CMU Sans Serif' fsize '10'
set output 'ir.svg'
# Color definitions
set border linewidth 1.5
set style line 1 lc rgb '#a0a0a0' lt 1 lw 2 pt 7 # gray
# Format graph
unset key
set xlabel 'Wavenumbers'
set ylabel 'Transmittance'
set xrange [4000:300]
# Plot data
plot 'spectrum.dat' with lines ls 1
This reverses the x-axis nicely, but I can't figure out how to change the scaling in such an unusual way.
As a chemist I am motivated to answer...
As far as I know gnuplot doesn't easily allow for arbitrary axis scaling (unless anyone has bright ideas about how to use set link). My strategy in this kind of situation is to plot the two halves separately and have them join seamlessly:
#!/usr/bin/env gnuplot
set terminal png size 800,500
set output 'ir.png'
set xlabel 'Wavenumbers' offset 20
set ylabel 'Transmittance'
set tics out nomirror
set key bottom right
set bmargin 4
set yrange [0:1]
set multiplot layout 1,2 title 'IR Spectrum of Cholesterol'
# left half of plot
set xrange [4000:2000]
set rmargin 0
set border 7
plot 'cholesterol.txt' notitle
# right half of plot
set xrange [1999:300]
set lmargin 0
set rmargin 2
set border 13
unset xlabel
unset ylabel
unset ytics
plot 'cholesterol.txt' title 'Cholesterol'
unset multiplot
My one quibble is that the 2000 is written twice and looks bolder on my screen, but I will leave fidgeting with the tics to you.
andyras' answer is a nice one, this is an arguably simpler (more elegant :-P) solution in terms of layout options. This should also be a more universal solution. If there are not too many tics (read below the figure if there are too many), then this could be done scaling the curve itself beyond 2000, and then adding all the tics by hand. Since I don't have IR spectrum data available I will use the dummy file "+" and plot log(x) from 4000 to 500:
xmax=4000 ; xmin = 500
pivot = 2000 ; rescfactor = 2.
rescale(x) = (x >= pivot ? x : pivot + rescfactor*(x-pivot))
set xrange [rescale(xmax):rescale(xmin)]
set xtics ("4000" 4000, "3000" 3000, "2000" 2000, \
"1500" rescale(1500), "1000" rescale(1000), "500" rescale(500))
plot "+" u (rescale($1)):(log($1)) w l
In your case you just substitute log($1) by 2 or whatever you're plotting.
In newer versions of gnuplot (starting from 4.4) adding the tics can be done automatically using a loop:
xmax = 4000 ; xmin = 500 ; step = 500
set xtics (sprintf("%i",xmax) rescale(xmax)) # Add the first tic by hand
set for [i=xmin:xmax-step:step] xtics add (sprintf("%i",i) rescale(i))
Starting from gnuplot 4.6 also a different for construction can be made using do for:
do for [i=xmin:xmax-step:step] {set xtics add (sprintf("%i",i) rescale(i))}
Title is pretty self explanatory but here is a picture of what I'd like to do. I'm having a tough time figuring out if its even possible.
Plot borrowed from:
Evaluation of geochemical background levels around sulfide mines – A new statistical procedure with beanplots. Gusstavason et al. 2012.
Doing the plot in exactly this orientation could be very cumbersome, if possible at all.
My suggestion is to plot everything with the usual orientation (i.e. having the 'sediments' axis as x-axis, or rather as x2-axis), rotate all labels a bit and finally rotate the complete output by 90 degree (pdf file with e.g. pdftk etc).
With this you can use any plot style as usual. In the script below I just show you how to plot the violet and yellow filled curves (using pseudo data) for two different data sets. Adding the other peaks should be straight forward (plot the bars with e.g. boxes or vector plotting style).
In order to have distinct ytics for the different plots, I associated a certain y-value with a certain plot, 1=Water, ..., 4=Gyttja).
Putting all toghether gives the following script:
reset
set terminal pdfcairo linewidth 2
outfile='bean'
set output outfile.'.pdf'
set encoding utf8
set x2range [0.5:9000]
set logscale x2
set x2tics (1, 5, 10, 50, '' 100, 500, '' 1000, 5000) out
set x2label 'mg/kg (sediments), µg/L (water)'
unset xtics
set yrange[0.5:4.5]
set ytics ('Water' 1, 'Minerogenic' 2, 'Peat' 3, 'Gyttja' 4) center rotate by -90 out
set label at graph 0.95, graph 0.05 right rotate by -90 'Nickel' font ',20' front
# cover possible data overlapping with the label
set object rectangle from graph 0.9, graph 0 to graph 1,graph 0.2 fillcolor rgb 'white' fillstyle solid noborder front
unset key
set macros
fs1="fillcolor rgb '#fc9e00' linewidth 2 fillstyle solid border lt -1"
fs2="fillcolor rgb '#9119f7' linewidth 2 fillstyle solid border lt -1"
# use pseudo data
set samples 500
plot '+' using 1:(4-0.3*exp(-(($1-10)/5.0)**4)) axes x2y1 with filledcurves y1=4 #fs1,\
'' using 1:(4+0.2*exp(-(($1-70)/50.0)**4)) axes x2y1 with filledcurves y1=4 #fs2,\
'' using 1:(1-0.4*exp(-(($1-5)/2.0)**2)) axes x2y1 with filledcurves y1=1 #fs1,\
'' using 1:(1+0.1*exp(-(($1-30)/20.0)**2)) axes x2y1 with filledcurves y1=1 #fs2
set output
system(sprintf('pdftk %s.pdf cat 1W output %s-rot.pdf', outfile, outfile))
system(sprintf('pdftocairo -r 150 -png %s-rot.pdf', outfile))
This gives (conventional and rotated output side-by-side) with 4.6.3:
Some stuff is required for the pseudo data. For a real data file, the plotting line looks a bit differently. The different plots have a separation of 1 in y-direction, so you must scale your data accordingly (done here manually with a scaling factor sc):
sc = 5.1
plot 'datafile.txt' using 1:(4 + $2/sc) axes x2y1 with filledcurves y1=4 #fs1
You can of course also do the scaling automatically, by extracting some minimum/maximum values using the stats command.
I am encountering problems while trying to create a 3D (2D mapped) graph.
The data I am generating should create a 3 dimensional normal distribution bump, or, when "mapped", it should look like a flattened 3D graph, with color used as the third dimension
The script I am using to generate the mapped graph is the following:
#!/usr/bin/gnuplot
reset
#set terminal png
set term postscript eps enhanced
set size square
set xlabel "X position"
set ylabel "Y position"
#set zlabel "Synaptic Strength"
#Have a gradient of colors from blue (low) to red (high)
set pm3d map
set palette rgbformulae 22,13,-31
#set xrange [0:110]
#set yrange [0:80]
#set zrange [0:1]
set style line 1 lw 1
#set title "Title"
#Don't want a key
unset key
#set the number of samples
set dgrid3d 51,51
set hidden3d
splot DataFile u 1:2:3
when I run it on the following DataFile (http://www.sendspace.com/file/ppibyw)
I get the following output
The legend indicates a z-range of 0-0.03, however, the datafile has far larger z-values, such as 0.1. Obviously I can't publish a graph that is so inaccurate. Furthermore, I need a better graph in order to gain a better insight as to what is wrong with my simulation.
Does anyone know why gnuplot handles 3d mapped graphs like this? I suspect it has to do with the number, and nature, of the samples.
You problem is in the set dgrid3d 51,51
Have a look at what happens if you write set dgrid3d 51,102 (much better) or set dgrid3d 51,500 (much worse)
The point is that (from the help)
The grid is equally spaced in x
(rows) and in y (columns); the z
values are computed as weighted
averages or spline interpolations of
the scattered points' z values. In
other words, a regularly spaced grid
is created and the a smooth
approximation to the raw data is
evaluated for all grid points. Only
this approximation is plotted, but
not the raw data.
You could try and improve the approximation if you want see the help (?dgrid3d), but I would rather just plot the data straight. You can do this by ditching the dgrid3d command altogether. You will have to modify your data file so that there is a blank line when the x coordinate changes. For example
3.10000000000000142109 4.15692193816530508599 0.00004084299890679580
3.10000000000000142109 4.33012701892219364908 0.00001123746243460237
3.15000000000000124345 0.08660254037844386521 0.00000816290100763514
3.15000000000000124345 0.25980762113533162339 0.00001935936190868058
Then with this simplified script
set terminal png![enter image description here][1]
#set size square
set xlabel "X position"
set ylabel "Y position"
#uncomment the next command to eliminate the mysterious glitch around x=3.4
set yrange [0.1:4.5]
set pm3d map
set output "grid_merged.png"
splot "grid_merged2.dat" u 1:2:3
set output
set term pop
I get
which is better than you get with the interpolated plot. I'm not sure what causes the glitch aroung 3.4, its not there on other (non-mapped) views - altering the yrange eliminates it - although I'm not sure it changing the y-range is cheating in terms of your simulation results....