I have a matrix which contains the atom numbers of the pairs of atoms which are in contact with each other. My matrix is like this:
column 1: atom number i;
column 2: atom number j
i,j runs from 1 to 800.
If there is a pair i-j in the matrix, place a dot corresponding to the position (i,j) of the matrix.
How do I plot such matrix?
Example:
A= [1,3; 3,8; 3,1; 6,2; 2,6; 1,2; 5,2; 8,3; 2,5; 2,1]
I want to Plot the matrix A, where X and Y-axis run from 1 to 8. Place a dot for every combination of X and Y which are present in A.
I want a plot like this:
Isn't this just a scatter plot?
If your m x 2 matrix is saved in a text file then this is trivial.
Here are the contents of an example data file "input.dat":
4 3
3 4
5 3
3 5
8 2
2 8
All you need to do is open the data file in xmgrace using xmgrace input.dat.
Now, initially it will be a line plot, but if you do 'Plot' > 'Set Appearance' and then with the only set already being selected you can set the 'Symbol Properties' 'Type:' to Diamond and 'Line Properties' 'Type:' to None you will already be on your way. Setting the symbol fill to solid red, tweaking the axis ranges and showing major tick grid lines will give a plot like the one you gave as an example.
You can save a parameters file and in future load the parameters at the beginning using
xmgrace -param template.par input2.dat.
But, having said all this, why not just plot it in matlab?
Related
I have a 3 column table named 'A' from which I want to plot a heatmap or scatter plot where I can see a colour for the coordinates indicated by the first two columns. For example, at row 'A91552' and column 's_4_AAGCTA' I want to see a colour corresponding to 0.47619.
Example data:
'A91552' 's_4_AAGCTA' 0.476190000000000
'A91554' 's_4_CCTATT' 0.476190000000000
's_4_AAGCTA' 'A91552' 0.476190000000000
's_4_CCTATT' 'A91554' 0.476190000000000
Is there a way to do this directly using the strings as indices, or will I need to make a double matrix and change the axis labels on something like imagesc?
Found it:
I just needed to convert my lists of strings to categorical variables:
scatter(categorical(A.Var1), categorical(A.Var2), 125, A.Var3, 'filled')
I have data in the format:
1 1 A
2 3 ab
1 2 A
3 3 x
4 1 x
2 3 A
and so on. The third column indicates the series. That is in the case above there are 3 distinct data series, one designated A, another designated ab and last designated x. Is there a way to plot the three data series from such data structure in gnuplot without using eg. awk? The difficulty here is that the number of categories (here denoted A, ab, x) is quite large and it is not feasible to write them out by hand.
I was thinking along the lines:
plot data u 1:2:3 w dots
but that does not work and I get warning: Skipping data file with no valid points (I tried quoted and unquoted version of the third column). A similar question has to manually define the palette which is undesirable.
With a little bit of work you can make a list of unique categories from within gnuplot without using external tools. The following code snippet first assembles a list of the entire third column of the data file, and then loops over it to generate a list of unique category names. If memory use or processing time become an issue then one could probably combine these steps and avoid forming a single string with the entire third column.
delimiter = "#" # some character that does not appear in category name
categories = ""
stats "test.dat" using (categories = categories." ".delimiter.strcol(3).delimiter) nooutput
unique_categories = ""
do for [cat in categories] {
if (strstrt (unique_categories, cat) ==0) {
unique_categories = unique_categories." ".cat
}
}
set xrange[0:5]
set yrange [0:4]
plot for [cat in unique_categories] "test.dat" using 1:(delimiter.strcol(3).delimiter eq cat ? $2 : NaN) title cat[2:strlen(cat)-1]
Take a look at the contents of the string variables categories and unique_categories to get a better idea of what this code does.
I have some values given by clock time, where the first column is the time. However, the values until 2 o clock still belong to the current day. Given
3 1
12 4
18 1
21 2
1 3
2 0
named as test.data, I'd like to print this in gnuplot:
set xrange [0:24]
plot 'test.data' with lines
However, the plot contains a backward line. It's striking through the whole diagram.
Is there a way to tell gnuplot to explicitly not print such backward lines, or even better, print them wrapping around the x axis (e.g. in my example drawing the line as a forward line up to 24, and then continuing it at 0)?
Note: The x axis of the plot should still start at 0 and end at 24.
As far as wrapping over the edge of the graph (a pac-man like effect), gnuplot can't do that on it's own. Even doing it manually, you would have to somehow calculate the right point to re-enter the graph based on the slope of the connecting line, and insert a new point into the data to control where the re-entry line enters, and where the exiting line exits. This would require external processing.
If you can do some outside preprocessing, adding a blank line before the 1 3 line will insert a discontinuity into the plot and prevent gnuplot from connecting those points (see help datafile for how gnuplot handles blank lines). Of course, you could always sort the data too.
I would recommend sorting the data before plotting, but if you do want to do this wrapping effect, the following python program (wrapper.py) will set up the data for it
data = [tuple(map(float,x.strip().split(" "))) for x in open("data.txt","r")]
data2 = sorted(data)
back_in_to = data2[0]
out_from = data2[-1]
xdelta = back_in_to[0] + 24 - out_from[0]
ydelta = back_in_to[1] - out_from[1]
slope = ydelta/xdelta
outy = out_from[1] + (24-out_from[0])*slope
print(0,outy)
for x in data2:
print(*x)
if x[0]==data[-1][0]: print("")
print(24,outy)
It reads in the data (assumed to be in data.txt, and calculates the points where a line should leave the graph and where it should re-enter, adding these points to the sorted data. It adds a blank line after the last point in the original graph, causing the break in the line. We can then plot like
plot "< wrapper.py" with lines
If we look at your original plot
we see the backward line that you referred to which reaches from the furthest right point to the next left point. The plot that the python program pre-processed reaches through the right of the graph to move back to this point.
Hello and good day to all
I have question related to excel graph. I have some set of values like this
Now I want to plot these values as a scatter graph. I want to to draw in such a way that by keeping X values same and 4 different Y plots i.e. A, B, C, D in a single graph. Meaning I dont want to merge these Y values on a single X value. Is there any way to do that? I thank you for your time and help.
The data does not make much sense. All X values are exactly the same, so all data markers will be at exactly the same X position.
To create a scatter chart with multiple series:
- select the data from A1 to B11
- insert a scatter chart
- select the B, C, D ranges (C1 to E11) and copy
- select the chart and use Paste Special > insert as new series with series name in first row
Since all X values are the same, many data points overlap and are not distinguishable.
Edit after comment: if you do NOT want to plot the values at their true X position (i.e. the value 1.4), then use four pairs of X / Y coordinates. Use X values 1 to 4 with A to D. Then use text boxes to replace the X axis labels or hide the labels and show the legend instead.
I have the following data, which I wan't to plot using GNUPLOT:
#TIME #VALUE #SOURCE
1 100 A
1 88 B
2 115 A
2 100 B
3 130 A
3 210 B
I want to have two lines drawn, depending on the value of column #SOURCE. One line for A and one line for B. Is this possible with GNUPLOT and if yes how?
Is it possible to also draw a summation of column #VALUE depending over column #TIME? Means, that for all equal entries in #TIME, the values in #VALUE will be summed up.
Thanks in advance,
Frank
One way to do it would be to use grep to locate lines ending with A or B and plot the result. You can do this in a single plot line with a for loop if you know the characters lines will end in:
plot for [s in 'A B'] sprintf("<(grep -v '%s$' data.dat)", s) u 1:2 w l
This plots the data you provided (saved in data.dat) as two different lines.
You could also change the for part to [s in 'word1 word2 word3'] or any other string you like. If you don't know the character/word lines will be ending with you would probably need to pass the file twice first to determine the string for the for loop and a second time to do the plotting.