I am trying to plot the following graph:
This plot was made using a command in R; however, I need to change the x-axis. As you see the x-axis starts at 0 and finish at 46. I want that the x-axis starts in 1972 and finishes in 2018 seq(1972, 2018). The data used for this graph is the following:
For regime one
structure(c(0.996336942021931, 0.982749831853788, 0.25257000136794,
0.707797489518183, 0.339372705184362, 0.999209103898399, 0.348786927897612,
0.821500770877589, 0.569473419352121, 0.544946043345147, 0.15347485404411,
0.987921203799956, 0.00247541125926418, 0.999925918450173, 0.996940249283586,
0.0141234625702467, 0.105466117156579, 0.999992944275275, 0.991723355647765,
0.0958472062267191, 0.0362729940372193, 0.999999790503447, 0.0750715811130157,
0.999975836828039, 0.998991768987905, 0.327943641159186, 5.05723080618291e-05,
0.999999999869691, 0.995538324405397, 0.123355227931813, 0.999776636825943,
0.00875781169836433, 0.696284480883101, 0.854839147672286, 0.113243492249383,
0.00984853715078062, 0.442061195271808, 0.999959859676686, 0.0249739384218217,
0.715262186931097, 0.269481397703521, 0.708458897302807, 0.0444979324520481,
0.000133950914911277, 0.997976154782607, 0.191386380576805, 0.99775339928206,
0.97921531595208, 0.27690132186733, 0.671995422154737, 0.458800347851363,
0.999155966774432, 0.417000082142666, 0.838969001100901, 0.576424593247709,
0.439169303472056, 0.227227711549776, 0.978527102362448, 0.00408165810824898,
0.999955057843957, 0.994643622809094, 0.00847570472458959, 0.163000467960203,
0.999995704786608, 0.987482614312069, 0.0569007267419926, 0.0585312256476362,
0.999999671060746, 0.118213072794827, 0.99998536150034, 0.998897081324845,
0.212968271334585, 8.35316288758489e-05, 0.999999999920876, 0.993537683112221,
0.188538497918178, 0.999604116439039, 0.00905848219612739, 0.769430430615986,
0.794457999021984, 0.0665707154963958, 0.00776458004359329, 0.5668500474175,
0.999931021995446, 0.0265573724408095, 0.661699294173752, 0.296009575623967,
0.587638579198176, 0.0251758869152202, 0.000220356219397782,
0.997352716237698, 0.191386380576805), .Dim = c(46L, 2L))
for regime 2:
structure(c(0.00366305797806813, 0.0172501681462116, 0.74742999863206,
0.292202510481817, 0.660627294815638, 0.000790896101601132, 0.651213072102388,
0.178499229122411, 0.430526580647879, 0.455053956654853, 0.846525145955889,
0.0120787962000438, 0.997524588740736, 7.40815498269273e-05,
0.00305975071641352, 0.985876537429753, 0.894533882843421, 7.05572472485335e-06,
0.00827664435223535, 0.904152793773281, 0.963727005962781, 2.09496553467159e-07,
0.924928418886985, 2.41631719608902e-05, 0.00100823101209502,
0.672056358840815, 0.999949427691938, 1.30308744399533e-10, 0.00446167559460289,
0.876644772068187, 0.00022336317405711, 0.991242188301636, 0.303715519116899,
0.145160852327714, 0.886756507750617, 0.990151462849219, 0.557938804728191,
4.01403233139628e-05, 0.975026061578178, 0.284737813068903, 0.730518602296479,
0.291541102697193, 0.955502067547952, 0.999866049085089, 0.00202384521739295,
0.808613619423195, 0.00224660071793958, 0.0207846840479196, 0.72309867813267,
0.328004577845263, 0.541199652148637, 0.000844033225568314, 0.582999917857334,
0.161030998899099, 0.423575406752291, 0.560830696527944, 0.772772288450224,
0.0214728976375518, 0.995918341891751, 4.49421560426429e-05,
0.00535637719090558, 0.99152429527541, 0.836999532039797, 4.29521339242403e-06,
0.0125173856879312, 0.943099273258007, 0.941468774352364, 3.28939253926857e-07,
0.881786927205173, 1.46384996596921e-05, 0.00110291867515508,
0.787031728665414, 0.999916468371124, 7.91243531099699e-11, 0.00646231688777926,
0.811461502081822, 0.00039588356096145, 0.990941517803873, 0.230569569384014,
0.205542000978016, 0.933429284503604, 0.992235419956407, 0.4331499525825,
6.89780045536876e-05, 0.973442627559191, 0.338300705826248, 0.703990424376033,
0.412361420801824, 0.97482411308478, 0.999779643780602, 0.00264728376230197,
0.808613619423195), .Dim = c(46L, 2L))
I know that the red line can be plotted using geom_line but I do not know how can the black bars plot? maybe using geom_bar, and also how can I merge the plots?
Thanks for your help
It's actually plotted using base R (good old times), using your first data for For regime one:
plot(Regime1[,1],type="h",xaxt="n",ylab="",cex.axis=0.6,xlab="",xlim=c(0,46))
lines(Regime1[,2],col="red")
mtext("Smoothed Probabilities",2,padj=-5,col="red",cex=0.7)
mtext("Fitted Probabilities",4,padj=1,cex=0.7)
axis(side=1,at=c(0,20,46),labels=c(1972,1992,2018))
Your xaxis values are actually 0:46, so you turn off the x-axis ticks using xaxt="n", then with axis(), you put it at 0,20,46 with the labels 1972...
It also depends on your plotting device, so might have to change the padj parameter in the axis to adjust the axis labels. I guess you can check out post like this for base R plotting functions.
In ggplot2, I guess you just create a data.frame with the Index as the years you need, and you call geom_segment() to plot the vertical lines :
library(ggplot2)
Regime1 = data.frame(Regime1)
colnames(Regime1) = c("Fitted","Smoothed")
Regime1$index = 1:nrow(Regime1)+1972
ggplot(Regime1,aes(x=index))+
geom_segment(aes(xend=index,y=0,yend=Fitted,col="Fitted")) +
geom_line(aes(y=Smoothed,col="Smoothed")) + theme_minimal() +
scale_color_manual(values=c("black","red"))
For a ggplot2 solution, you are going to need a data.frame or tibble with 4 columns (Regime, Year, Smoothed, and Fitted). Based on the data you provided, this would have 92 rows.
Now assuming you use those column names (and storing your data into the variable example.dat), a ggplot2 solution is
example.dat %>%
ggplot( aes(x=Year) ) +
geom_line( aes(y=Smoothed), color="red" ) +
geom_linerange( aes(ymax=Fitted), ymin=0 ) +
facet_wrap( ~ Regime, ncol=1 )
Then you might need to adjust some of the scales to get the best plot.
I would like to create a stacked area chart, similar to this for example, in Julia using Plots.
I know / suppose that you can do this if you directly use the Gadfly or PyPlot backends in Julia, but I was wondering if there was a recipe for this. If not, how can you contribute to the Plots Recipes? Would be a useful addition.
There's a recipe for something similar in
https://docs.juliaplots.org/latest/examples/pgfplots/#portfolio-composition-maps
For some reason the thumbnail looks broken now though (but the code works).
The exact plot in the matlab example can be produced by
plot(cumsum(Y, dims = 2)[:,end:-1:1], fill = 0, lc = :black)
As a recipe that would look like
#userplot AreaChart
#recipe function f(a::AreaChart)
fillto --> 0
linecolor --> :black
seriestype --> :path
cumsum(a.args[1], dims = 2)[:,end:-1:1]
end
If you want to contribute a recipe to Plots you can open a pull request on Plots, or, eg. on StatsPlots - there's a good description of contributing here: https://docs.juliaplots.org/latest/contributing/
It's a bit of reading, but very generally useful as an introduction to contributing to Julia packages.
You can read this thread in the Julia discourse forum where the question is developed in deep.
One solution posted there using Plots is :
# a simple "recipe" for Plots.jl to get stacked area plots
# usage: stackedarea(xvector, datamatrix, plotsoptions)
#recipe function f(pc::StackedArea)
x, y = pc.args
n = length(x)
y = cumsum(y, dims=2)
seriestype := :shape
# create a filled polygon for each item
for c=1:size(y,2)
sx = vcat(x, reverse(x))
sy = vcat(y[:,c], c==1 ? zeros(n) : reverse(y[:,c-1]))
#series (sx, sy)
end
end
a = [1,1,1,1.5,2,3]
b = [0.5,0.6,0.4,0.3,0.3,0.2]
c = [2,1.8,2.2,3.3,2.5,1.8]
sNames = ["a","b","c"]
x = [2001,2002,2003,2004,2005,2006]
plotly()
stackedarea(x, [a b c], labels=reshape(sNames, (1,3)))
(by user NiclasMattsson)
Other ways presented there include using the VegaLite.jl package.
I cannot find anything in documentation here.
Code
library("Vennerable")
data(StemCell)
Vstem <- Venn(StemCell)
Vstem3 <- Vstem[, c("OCT4", "SOX2", "NANOG")]
tl <- "masi"
plot(Vstem3, doWeights = TRUE, type = "circles")
Tried unsuccessfully
plot(..., main = tl)
plot(..., title = tl)
plot(...); title(tl)
plt <- plot(...); title(plt, tl)
Fig. 1 Wrong output without title
R: 3.3.1
OS: Debian 8.5
user20650 answer in comments summarised here. Try (1-2) and choose what fits best.
The plot method is based on the grid package so the normal base R plot approaches to add a title won't work. Looking at the arguments of args(Vennerable:::plotVenn), there doesn't seem a way to add a title and unhelpfully the plots do not return a grid object. So you can just draw a title on the plot window with the following
grid.text("masi", y=0.9, gp=gpar(col="red", cex=2))
As an alternative method, you could grab the grob and then use grid.arrange to plot the title
gridExtra::grid.arrange(grid::grid.grabExpr(plot(Vstem3, doWeights = TRUE,
type = "circles")), top="masi")
The grid.arrange way adds the title as a separate grob, and then they are arranged in two rows. So when resizing the graphics window, it still appears above the plot. This won't be true when drawing straight on the window (as in the first version).
Note: you do not need to use gridExtra, you could do this in grid.
Fig. 1 Output from (1),
Fig. 2 Output from (2)
I think (1) could be better with more adjustments, but now (2) is better.
I am using a package(LightGraphs.jl) in Julia, and it has a predefined histogram method that creates the degree distribution of a network g.
deg_hist = degree_histogram(g)
I want to make a plot of this but i am new to plotting in Julia. The object returned is a StatsBase.Histogram which has the following as its inner fields:
StatsBase.Histogram{Int64,1,Tuple{FloatRange{Float64}}}
edges: 0.0:500.0:6000.0
weights: [79143,57,32,17,13,4,4,3,3,2,1,1]
closed: right
Can you help me how I can make use of this object to plot the histogram?
I thought this was already implemented, but I just added the recipe to StatPlots. If you check out master, you'll be able to do:
julia> using StatPlots, LightGraphs
julia> g = Graph(100,200);
julia> plot(degree_histogram(g))
For reference, the associated recipe that I added to StatPlots:
#recipe function f(h::StatsBase.Histogram)
seriestype := :histogram
h.edges[1], h.weights
end
Use the histogram fields .edges and .weights to plot it e.g.
using PyPlot, StatsBase
a = rand(1000); # generate something to plot
test_hist = fit(Histogram, a)
# line plot
plot(test_hist.edges[1][2:end], test_hist.weights)
# bar plot
bar(0:length(test_hist.weights)-1, test_hist.weights)
xticks(0:length(test_hist.weights), test_hist.edges[1])
or you could create/extend a plotting function adding a method like so:
function myplot(x::StatsBase.Histogram)
... # your code here
end
Then you will be able to call your plotting functions directly on the histogram object.
Hopefully a straightforward question but I made a simple figure in R using filled.contour(). It looks fine, and what it should like given the data. However, I want to add a reference line along a contour for 0 (level = 0), and the plotted line doesn't match the colors on the filled.contour figure. The line is close, but not matching with the figure (and eventually crossing over another contour from the filled.contour plot). Any ideas why this is happening?
aa <- c(0.05843150, 0.11300040, 0.15280030, 0.183524400, 0.20772430, 0.228121000)
bb <- c(0.01561055, 0.06520635, 0.10196237, 0.130127650, 0.15314544, 0.172292410)
cc <- c(-0.02166599, 0.02306650, 0.05619421, 0.082193680, 0.10334837, 0.121156780)
dd <- c(-0.05356592, -0.01432910, 0.01546647, 0.039156660, 0.05858709, 0.074953650)
ee <- c(-0.08071987, -0.04654243, -0.02011676, 0.000977798, 0.01855881, 0.033651089)
ff <- c(-0.10343798, -0.07416114, -0.05111547, -0.032481132, -0.01683215, -0.003636035)
gg <- c(-0.12237798, -0.09753544, -0.07785126, -0.061607548, -0.04788856, -0.036169540)
hh <-rbind(aa,bb,cc,dd,ee,ff,gg)
z <- as.matrix(hh)
y <- seq(0.5,1.75,0.25)
x <- seq(1,2.5,0.25)
filled.contour(x,y,z,
key.title = title(main=expression("log"(lambda))),
color.palette = topo.colors) #This works
contour(x,y,z, level=0,add=T,lwd=3) #This line doesn't match plot
This is completely answered in the ?filled.contour help page. In the Notes section it states
The output produced by filled.contour is actually a combination of two plots; one is the filled contour and one is the legend. Two separate coordinate systems are set up for these two plots, but they are only used internally – once the function has returned these coordinate systems are lost. If you want to annotate the main contour plot, for example to add points, you can specify graphics commands in the plot.axes argument. See the examples.
And the examples given in that help page show how to annotate on top of the main plot. In this particular case, the correct way would be
filled.contour(x,y,z,
key.title = title(main=expression("log"(lambda))),
color.palette = topo.colors,
plot.axes = {
axis(1)
axis(2)
contour(x,y,z, level=0,add=T,lwd=3)
}
)
which produces