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I am trying to replicate something close to the following graph in gnuplot as I need to use it on a latex paper. I have tried a lot but I cannot make the two-line labels at the bottom. Could you please guide me? Also, how is it possible to have the % character as part of a label in the x-axis? Latex complains about it.
The data are in the following format (example). Each different color corresponds to different method. Blue is method 1 (m1), orange is method 2 (m2), and brown is method 3 (m3)
#% system1-m1 system1-m2 system1-m3 system2-m1 ...
0.5% 16 8 15 6
1% 15 17 16 8
2% 12 10 20 15
Thanks
Edit
My code so far is as follows:
set rmargin 0
set key outside tmargin center top horizontal width 3
set border
set grid
set boxwidth 0.8
set style fill solid 1.00
set xtics nomirror rotate by 0
set format y '%1.f'
set yrange [0 to 22]
set ylabel 'Gain (\%)'
set ytics 0, 5
set style data histograms
set label 1 at -0.3, -4 '|---------System 1------------|'
set label 2 at 2.7, -4 '|---------System 2------------|'
plot "./data/metrics.dat" using 2:xtic(1) title 'Method 1' ,\
"" using 3 title 'Method 2', \
"" using 4 title 'Method 3',
And I have modified the .dat file as
0.5 16 8 15
1.0 15 17 16
2.0 12 10 20
0.5 13 6 4
1.0 11 13 13
2.0 14 12 14
because I cannot make it print the % character. The output graph is
As you can see it is not scalable. I have to put labels by hand (trial and error) and also the labels below the x-axis do not contain the % character.
We've been close: set format x '%.1f\%%'. The following works for me with cairolatex terminal (check help cairolatex).
Code:
### percent sign for tic label in TeX
reset session
set term cairolatex
set output 'SO70029830.tex'
set title 'Some \TeX\ or \LaTeX\ title: $a^2 + b^2 = c^2$'
set format x '%.1f\%%'
plot x
set output
### end of code
Result: (screenshot)
Addition:
Sorry, I forgot the second part of your question: the labels.
Furthermore, in your graph you are using xtic(1) as tic labels, i.e. text format, so the command set format x '%.1f\%%' from my answer above will not help here. One possible solution would be to create and use your special TeX label like this:
myTic(col) = sprintf('%.1f\%%',column(col))
plot $Data using 2:xtic(myTic(1))
For the labels, I would use arrows and labels. Each histogram is placed at integer numbers starting from 0. So, the arrows have to go from x-values -0.5 to 2.5 and from 2.5 to 5.5. The labels are placed at x-value 1 and 4. There is certainly room for improvements.
Code:
### tic labels with % for TeX and lines/labels
reset session
set term cairolatex
set output 'SO70029830.tex'
$Data <<EOD
0.5 16 8 15
1.0 15 17 16
2.0 12 10 20
0.5 13 6 4
1.0 11 13 13
2.0 14 12 14
EOD
set rmargin 0
set key outside center top horizontal width 3
set border
set grid
set boxwidth 0.8
set style fill solid 1.00
set xtics nomirror rotate by 0
set format y '%1.f'
set yrange [0 to 22]
set ylabel 'Gain (\%)'
set ytics 0, 5
set style data histograms
set bmargin 4
set arrow 1 from -0.5, screen 0.05 to 2.5, screen 0.05 heads size 0.05,90
set label 1 at 1, screen 0.05 'System 1' center offset 0,-0.7
set arrow 2 from 2.5, screen 0.05 to 5.5, screen 0.05 heads size 0.05,90
set label 2 at 4, screen 0.05 'System 2' center offset 0,-0.7
myTic(col) = sprintf('%.1f\%%',column(col))
plot $Data using 2:xtic(myTic(1)) title 'Method 1' ,\
"" using 3 title 'Method 2', \
"" using 4 title 'Method 3',
set output
### enf of code
Result: (screenshot from LaTeX document)
As an alternative to the answer of #theozh there is already a build-in function called newhistogram that directly allows to place labels below the x-axis.
While working on an an answer that involves newhistogram I discovered a bug with horizontal key layout, which is now fixed thanks to Ethan. So, with the newest development version of gnuplot at hand I am able to offer a solution that allows for more finetuning like the ability to change the inter-group spacing.
set terminal cairolatex standalone colour header '\usepackage{siunitx}' size 25cm, 7cm
# generate some random data in your format
N = 7
set print $MYDATA
do for [i=1:N] {
print sprintf('0.5 %f %f %f', rand(0)*20, rand(0)*20, rand(0)*20)
print sprintf('1.0 %f %f %f', rand(0)*20, rand(0)*20, rand(0)*20)
print sprintf("2.0 %f %f %f", rand(0)*20, rand(0)*20, rand(0)*20)
}
unset print
# define the look
set style data histograms
set style fill solid 1.00
set boxwidth 0.8
set key horizontal outside t c width 1
set xr [-1:27]
set xtics nomirror
set ytics out 5 nomirror
set grid y # I don't think vertical grid lines are needed here
set ylabel 'Gain/\%'
set rmargin 0.01
set bmargin 3
As for the tic marks, I adapted #theozh's answer a bit – since you are using LaTeX already, you might as well parse the numbers through siunitx, which will ensure correct spacing between numbers and the unit:
myTic(col) = sprintf('\SI{%.1f}{\%}',column(col))
The vertical separation marks like in the screenshot you provided can be created iteratively:
do for [i=1:N+1] {set arrow i from first -1+(i-1)*4, graph 0 to first -1+(i-1)*4, screen 0 lw 2 nohead}
Now for the actual plot command:
plot newhistogram "System 1" offset 0,-0.5 lt 1, for [i=1:3] $MYDATA using (column(i+1)):xtic(myTic(1)) every ::0::2 title sprintf('Method %.0f',i), \
newhistogram "System 2" offset 0,-0.5 lt 1 at 4, for [i=1:3] $MYDATA using (column(i+1)):xtic(myTic(1)) every ::3::5 not, \
newhistogram "System 3" offset 0,-0.5 lt 1 at 8, for [i=1:3] $MYDATA using (column(i+1)):xtic(myTic(1)) every ::6::8 not, \
newhistogram "System 4" offset 0,-0.5 lt 1 at 12, for [i=1:3] $MYDATA using (column(i+1)):xtic(myTic(1)) every ::9::11 not, \
newhistogram "System 5" offset 0,-0.5 lt 1 at 16, for [i=1:3] $MYDATA using (column(i+1)):xtic(myTic(1)) every ::12::14 not, \
newhistogram "System 6" offset 0,-0.5 lt 1 at 20, for [i=1:3] $MYDATA using (column(i+1)):xtic(myTic(1)) every ::15::17 not, \
newhistogram "System 7" offset 0,-0.5 lt 1 at 24, for [i=1:3] $MYDATA using (column(i+1)):xtic(myTic(1)) every ::18::20 not
That looks very nasty, what's going on here?
newhistogram creates a new group of histogram boxes, its first argument is a string that is put below the x axis. It is also told to reset the linetype counter to 1.
Then the three columns of the data are plotted iteratively, but not all lines at once, but only the first three lines, with corresponding key entries.
Then another newhistogram is created and it is told to start at the x value 4 (which would be the default anyway). Now the next three lines are plotted, and so.
Now, every time newhistogram is called an empty line is added to key, hence making trouble with the key placement. Therefore the new keyword introduced by Ethan is
set style histogram nokeyseparators
which will disable this behaviour.
As you see, the spaces between the groups are larger than inside. You might want to change the numbers in newhistogram at ... and adjust the calculation of vertical line positions accordingly.
The plot command is of course highly repetitive, and it would be nice to make it an iterative call. Unfortunately, iterations that span multiple objects are not possible within a plot call. However, it is possible to iteratively put the plot command string together (excessively using string concatenation .) and then plot it.
A = 'newhistogram "System '
B = '" offset 0,-0.5 lt 1'
C = 'for [i=1:3] $MYDATA using (column(i+1)):xtic(myTic(1)) every ::'
myplotstring = A.'1'.B.', '.C."0::2 title sprintf('Method %.0f',i),"
do for [i=2:N] {myplotstring = myplotstring.A.i.B.'at '.(4*(i-1)).', '.C.(3*i-3).'::'.(3*i-1).' not, '}
plot #myplotstring
I am trying to capture some data in TCL. I have below data :
{0.0 0.0} {0.741 0.48}
My required out put is 3rd column of this data.
0.741
how can i achieve it?
set oaDesign [ed]
set rprb [db::getShapes -of $oaDesign -lpp {INST_B drawing}]
set r [de::getBBox $rprb]
puts $r
{0.0 0.0} {0.741 0.48}
I just need 3rd column, which is 0.741
You would use lindex and lset, respectively, to access the nested list's elements at a known position:
% lindex $r 1 0
0.741
To write back into that list of lists, at a given position:
% lset r 1 0 0.0
{0.0 0.0} {0.0 0.48}
Did you search SO for previous answers, before raising your question?
I am using BehaviorSpace to run the model hundreds of times with different parameters. But I need to know the locations of all turtles as a result instead of only the number of turtles. How can I achieve it with BehaviorSpace?
Currently, I output the results in a csv file by this code:
to-report get-locations
report (list xcor ycor)
end
to generate-output
file-open "model_r_1.0_locations.csv"
file-print csv:to-row get-locations
file-close
end
but all results are popped into same csv file, so I can't tell the condition of each running.
Seth's suggestion of incorporating behaviorspace-run-number in the filename of your csv output is one alternative. It would allow you to associate that file with the summary data in your main BehaviorSpace output file.
Another option is to include list reporters as "measures" in your behavior space experiment definition. For example, in your case:
map [ t -> [ xcor ] of t ] sort turtles
map [ t -> [ ycor ] of t ] sort turtles
You can then parse the resulting list "manually" in your favourite data analysis language. I've used the following function for this before, in Julia:
parselist(strlist, T = Float64) = parse.(T, split(strlist[2:end-1]))
I'm sure you can easily write some equivalent code in Python or R or whatever language you're using.
In the example above, I've outputted separate lists for the xcor and the ycor of turtles. You could also output a single "list of lists", but the parsing would be trickier.
Edit: How to do this using the csv extension and R
Coincidentally, I had to do something similar today for a different project, and I realized that a combination of the csv extension and R can make this very easy.
The general idea is the following:
In NetLogo, use csv:to-string to encode list data into a string and then write that string directly in the BehaviorSpace output.
In R, use purrr::map and readr::read_csv, followed by tidyr::unnest, to unpack everything in a neat "one observation per row" dataframe.
In other words: we like CSV, so we put CSV in our CSV so we can parse while we parse.
Here is a full-fledged example. Let's say we have the following NetLogo model:
extensions [ csv ]
to setup
clear-all
create-turtles 2 [ move-to one-of patches ]
reset-ticks
end
to go
ask turtles [ forward 1 ]
tick
end
to-report positions
let coords [ (list who xcor ycor) ] of turtles
report csv:to-string fput ["who" "x" "y"] coords
end
We then define the following tiny BehaviorSpace experiment, with only two repetitions and a time limit of two, using our positions reporter as an output:
The R code to process this is pleasantly straightforward:
library(tidyverse)
df <- read_csv("experiment-table.csv", skip = 6) %>%
mutate(positions = map(positions, read_csv)) %>%
unnest()
Which results in the following dataframe, all neat and tidy:
> df
# A tibble: 12 x 5
`[run number]` `[step]` who x y
<int> <int> <int> <dbl> <dbl>
1 1 0 0 16 10
2 1 0 1 10 -2
3 1 1 1 9.03 -2.24
4 1 1 0 -16.0 10.1
5 1 2 1 8.06 -2.48
6 1 2 0 -15.0 10.3
7 2 0 1 -14 1
8 2 0 0 13 15
9 2 1 0 14.0 15.1
10 2 1 1 -13.7 0.0489
11 2 2 0 15.0 15.1
12 2 2 1 -13.4 -0.902
The same thing in Julia:
using CSV, DataFrames
df = CSV.read("experiment-table.csv", header = 7)
cols = filter(col -> col != :positions, names(df))
df = by(df -> CSV.read(IOBuffer(df[:positions][1])), df, cols)
In Python, it's possible to count items in list using a high-performance object collections.Counter:
>>> from collections import Counter
>>> l = [1,1,2,4,1,5,12,1,51,2,5]
>>> Counter(l)
Counter({1: 4, 2: 2, 5: 2, 4: 1, 12: 1, 51: 1})
I've search in http://docs.julialang.org/en/latest/search.html?q=counter but I can't seem to find a counter object.
I've also looked at http://docs.julialang.org/en/latest/stdlib/collections.html but I couldn't find it either.
I've tried the histogram function in Julia and it returned a wave of deprecation messages:
> l = [1,1,2,4,1,5,12,1,51,2,5]
> hist(l)
[out]:
WARNING: sturges(n) is deprecated, use StatsBase.sturges(n) instead.
in depwarn(::String, ::Symbol) at ./deprecated.jl:64
in sturges(::Int64) at ./deprecated.jl:623
in hist(::Array{Int64,1}) at ./deprecated.jl:646
in include_string(::String, ::String) at ./loading.jl:441
in execute_request(::ZMQ.Socket, ::IJulia.Msg) at /Users/liling.tan/.julia/v0.5/IJulia/src/execute_request.jl:175
in eventloop(::ZMQ.Socket) at /Users/liling.tan/.julia/v0.5/IJulia/src/eventloop.jl:8
in (::IJulia.##13#19)() at ./task.jl:360
while loading In[65], in expression starting on line 1
WARNING: histrange(...) is deprecated, use StatsBase.histrange(...) instead
in depwarn(::String, ::Symbol) at ./deprecated.jl:64
in histrange(::Array{Int64,1}, ::Int64) at ./deprecated.jl:582
in hist(::Array{Int64,1}, ::Int64) at ./deprecated.jl:645
in hist(::Array{Int64,1}) at ./deprecated.jl:646
in include_string(::String, ::String) at ./loading.jl:441
in execute_request(::ZMQ.Socket, ::IJulia.Msg) at /Users/liling.tan/.julia/v0.5/IJulia/src/execute_request.jl:175
in eventloop(::ZMQ.Socket) at /Users/liling.tan/.julia/v0.5/IJulia/src/eventloop.jl:8
in (::IJulia.##13#19)() at ./task.jl:360
while loading In[65], in expression starting on line 1
WARNING: hist(...) and hist!(...) are deprecated. Use fit(Histogram,...) in StatsBase.jl instead.
in depwarn(::String, ::Symbol) at ./deprecated.jl:64
in #hist!#994(::Bool, ::Function, ::Array{Int64,1}, ::Array{Int64,1}, ::FloatRange{Float64}) at ./deprecated.jl:629
in hist(::Array{Int64,1}, ::FloatRange{Float64}) at ./deprecated.jl:644
in hist(::Array{Int64,1}, ::Int64) at ./deprecated.jl:645
in hist(::Array{Int64,1}) at ./deprecated.jl:646
in include_string(::String, ::String) at ./loading.jl:441
in execute_request(::ZMQ.Socket, ::IJulia.Msg) at /Users/liling.tan/.julia/v0.5/IJulia/src/execute_request.jl:175
in eventloop(::ZMQ.Socket) at /Users/liling.tan/.julia/v0.5/IJulia/src/eventloop.jl:8
in (::IJulia.##13#19)() at ./task.jl:360
while loading In[65], in expression starting on line 1
**Is there a Counter object in Julia?**
If you are using Julia 0.5+, the histogram functions has been deprecated and you are supposed to use the StatsBase.jl module instead. It is also described in the warning:
WARNING: hist(...) and hist!(...) are deprecated. Use fit(Histogram,...) in StatsBase.jl instead.
But if you are using StatsBase.jl, probably countmap is closer to what you need:
julia> import StatsBase: countmap
julia> countmap([1,1,2,4,1,5,12,1,51,2,5])
Dict{Int64,Int64} with 6 entries:
4 => 1
2 => 2
5 => 2
51 => 1
12 => 1
1 => 4
The DataStructures.jl package also has Accumulators / Counters with a more
general set of methods for using and combining counters.
Once you've added the package
using Pkg
Pkg.add("DataStructures")
you can count the elements of a sequence by constructing a counter
# generate some data to count
using Random
seq = [ Random.randstring('a':'c', 2) for _ in 1:100 ]
# count the elements in seq
using DataStructures
counts = counter(seq)
I should probably delete this question, since I found an answer elsewhere on stackoverflow.
Using 'Vectorize' solved the problem.
outer(x,y,Vectorize(model))
I'll leave this up for a bit in case this helps anyone else. The issue I had is described below.
I am an occasional user of R, mostly for Scientific Programming. I want to evaluate a function on a grid of x,y values. Something similar to this simple example:
> x=seq(1,5,1)
> y=seq(1,5,1)
> model = function(a,b){a+b}
> (outer(x,y,model))
[,1] [,2] [,3] [,4] [,5]
[1,] 2 3 4 5 6
[2,] 3 4 5 6 7
[3,] 4 5 6 7 8
[4,] 5 6 7 8 9
[5,] 6 7 8 9 10
The input and output of my actual function looks like this (the volumetric flow rate of a 'Cross' fluid in a circular pipe):
> SimpleCrossModelCircPipe(eta_0 = 176.45, lambda = 2.4526, m=0.83122, mesh=1000,
pipe_length=1.925, press_drop=20.3609, pipe_diameter=0.0413)
[1] 0.005635064
I want to evaluate the function on a grid of values, for example, press_drop and pipe_diameter. So, define a function of these two variables.
> model = function(a,b){SimpleCrossModelCircPipe(eta_0 = 176.45, lambda = 2.4526,
m=0.83122, mesh=1000,pipe_length=1.925, press_drop=a, pipe_diameter=b)}
For just one pair of values this does work:
> model(1,2)
[1] 107249.8
But, if I use with 'outer', there is an error.
> (outer(x,y,model))
Error in seq.default(tau_wall, 0, length.out = mesh + 1) :
'from' must be of length 1
If I place a print statement for the local variable, tau_wall, using outer generates all 25 values, before moving to the line, which generates the error, since tau_wall should have length 1, not 25.
(outer(x,y,model))
[1] 352.5289 705.0579 1057.5868 1410.1158 1762.6447 705.0579 1410.1158 2115.1736
[9] 2820.2315 3525.2894 1057.5868 2115.1736 3172.7605 4230.3473 5287.9341 1410.1158
[17] 2820.2315 4230.3473 5640.4630 7050.5788 1762.6447 3525.2894 5287.9341 7050.5788
[25] 8813.2235
Is there a simple fix to make this work?
Best,
Steve