If you just want to limit the axis just insert as arguments for the x axis xlim = c(min, max), and for the y ylim = c(min,max) , where min and max correspond to the appropriate min and max for the x and y axes
As for the panel.groups you mention medians where I was using means - if you want medians you will have to amend means to medians Make sure for the groups you have the right mode numeric/ factor ? I do not know what igra is Duncan -----Original Message----- From: Luigi Marongiu [mailto:marongiu.lu...@gmail.com] Sent: Thursday, 1 May 2014 03:54 To: Duncan Mackay Subject: Re: [R] set axis limit in lattice Dear Duncan, these solutions are actually splitting the drawing in different panels and the scale=free is giving different limits to each panel. I still need the relation=same but just to input myself the fixed limits of the axis. It should go into the scale argument but i don't know the actual syntax. As for the segments, you were perfectly right, there was a problem with my script so the medians did not match the actual data. Your solution using panel.groups works on the example, but when I copied it to the actual dataframe I am working with it did not work despite the fact of being of quite a general syntax. could you please give a look at the dataframe I have attached and see where I made a mistake in applying your solution? what I wrote is: my.data.IP10<-subset(my.data, gene=="i" & stimulus != "Unstimulated") stripplot( my.data.IP10$ratio ~ factor(my.data.IP10$igra)|factor(my.data.IP10$stimulus, levels = c("ESAT6","CFP10","Rv3615c", "Rv2654","Rv3879", "Rv3873","PHA")), my.data, group = my.data.IP10$igra, hor=F, layout = c(7,1), scales = list(x = list(draw=FALSE)), jitter.data=TRUE, pch=c(1,16), col="black", ylab=expression(bold("Ratio GOI/RG")), xlab=expression(bold("Antigen stimulation")), main="IP10 expression", par.settings = list(strip.background=list(col="light grey")), par.strip.text=list(font=2), key = list(space="top", columns=2, text=list(c("IGRA Negative", "IGRA Positive"), col="black"), points=list(pch=c(1,16), col="black")), panel = panel.superpose, panel.groups = function(x, y, group.number, ...) { panel.segments(x0= x-0.25, x1=x+0.25, y0=mean(y), y1=mean(y), lty = c(1:2)[group.number], lwd=c(2:1)[group.number], col = c(1:2)[group.number]) panel.stripplot(x,y, ...) } ) ### Many thanks ### Best regards Luigi On Wed, Apr 30, 2014 at 12:15 AM, Duncan Mackay <dulca...@bigpond.com> wrote: > Hi Luigi > > This produces plenty of white space for the y axes > > Y<-max(my.data$copy) > > stripplot( > copy ~ factor(positivity)|factor(stimulation, levels = c("Unst.", > "ESAT6","CFP10","Rv3615c", "Rv2654","Rv3879", "Rv3873","PHA")), > my.data, > group = positivity, > hor=F, > layout = c(8,1), > scales = list(x = list(at = c(1,2), labels = c("N","P")), > y= list(relation = "free")), > jitter.data=TRUE, pch=c(16,1), col="black", > ylab=expression(bold("Copy")), > xlab=expression(bold("Stimulation")), > main="Plot", > par.settings = list(strip.background=list(col="white")), > par.strip.text=list(font=2), > key = key.plot, > panel = function(x, y, ...) > { > pnl = panel.number() > k<-0 > for (i in 1:2){ > datme<-subset(datmeA, positivity==i-1) > w<-i+k > panel.segments(x0 = X[w], y0 = datme[datme[,2]== > levels(datme[,2])[pnl],"copy"], > x1 = X[w+1], y1 = datme[datme[,2]== > levels(datme[,2])[pnl],"copy"],lwd = 2, col = "black") > k=k+1 > > panel.stripplot(x,y, ...) > } > } > ) > You could limit the y-axis to your levels > stripplot( > copy ~ factor(positivity)|factor(stimulation, levels = c("Unst.", > "ESAT6","CFP10","Rv3615c", "Rv2654","Rv3879", "Rv3873","PHA")), > my.data, > group = positivity, > hor=F, > layout = c(8,1), > scales = list(x = list(at = c(1,2), labels = c("N","P")), > y= list(relation = "free", > limits = list(c(0, max panel 1), > c(0, max panel 2), > ... > c(0, max panel 8)), > )), > jitter.data=TRUE, pch=c(16,1), col="black", > ylab=expression(bold("Copy")), > xlab=expression(bold("Stimulation")), > main="Plot", > par.settings = list(strip.background=list(col="white")), > par.strip.text=list(font=2), > key = key.plot, > panel = function(x, y, ...) > { > pnl = panel.number() > k<-0 > for (i in 1:2){ > datme<-subset(datmeA, positivity==i-1) > w<-i+k > panel.segments(x0 = X[w], y0 = datme[datme[,2]== > levels(datme[,2])[pnl],"copy"], > x1 = X[w+1], y1 = datme[datme[,2]== > levels(datme[,2])[pnl],"copy"],lwd = 2, col = "black") > k=k+1 > > panel.stripplot(x,y, ...) > } > } > ) > > Sorting the stimulation groups shows that some of them can be loosely grouped > so reordering the factors > > stripplot(copy ~ factor(positivity)|factor(stimulation, levels = > c("PHA","Rv2654","CFP10","Unst.","Rv3615c", "Rv3873","ESAT6", "Rv3879")), > my.data, > group = positivity, > hor=F, > layout = c(2,4), > scales = list(x = list(at = c(1,2), labels = c("N","P")), > y= list(relation = "free")), > jitter.data=TRUE, pch=c(16,1), col="black", > ylab=expression(bold("Copy")), > xlab=expression(bold("Stimulation")), > main="Plot", > par.settings = list(strip.background=list(col="white")), > par.strip.text=list(font=2), > key = key.plot, > panel = function(x, y, ...) > { > pnl = panel.number() > k<-0 > for (i in 1:2){ > datme<-subset(datmeA, positivity==i-1) > w<-i+k > panel.segments(x0 = X[w], y0 = datme[datme[,2]== > levels(datme[,2])[pnl],"copy"], > x1 = X[w+1], y1 = datme[datme[,2]== > levels(datme[,2])[pnl],"copy"],lwd = 2, col = "black") > k=k+1 > > panel.stripplot(x,y, ...) > } > } > ) > > or using panel.groups > > stripplot(copy ~ factor(positivity)|factor(stimulation, levels = > c("PHA","Rv2654","CFP10","Unst.","Rv3615c", "Rv3873","ESAT6", "Rv3879")), > my.data, > group = positivity, > hor=F, > layout = c(2,4), > scales = list(x = list(at = c(1,2), labels = c("N","P")), > y= list(relation = "free")), > jitter.data=TRUE, pch=c(16,1), col="black", > ylab=expression(bold("Copy")), > xlab=expression(bold("Stimulation")), > main="Plot", > par.settings = list(strip.background=list(col="white")), > par.strip.text=list(font=2), > key = key.plot, > panel = panel.superpose, > panel.groups = function(x, y, group.number, ...) { > > panel.segments(x0= x-0.25, x1=x+0.25, y0=mean(y), > y1=mean(y), lty = c(1:2)[group.number], > lwd=c(2:1)[group.number], col = c(1:2)[group.number]) > > panel.stripplot(x,y, ...) > } > ) > > Regards > > Duncan Mackay > > -----Original Message----- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On > Behalf Of Luigi Marongiu > Sent: Wednesday, 30 April 2014 03:58 > To: r-help@r-project.org > Subject: [R] set axis limit in lattice > > Dear all, > > I would like to set the axis of a figure using the max() so to have > more control on the limits of the axis -- this because in the actual > case more independent figures are generated from the same dataframe > and these must have the same axis scale. > > Since the figure is generated using lattice device, the syntax is too > complicated for me: when I place the xlim=c(0,Y) in the arguments — > where Y is obtained using max(data) — there is no result. In basic R > this argument would work virtually in any position. > > Any tip? > > Best regards > > Luigi > > ####CODE > ### open plot library > library(lattice) > my.data<-structure(list( > column_1 = 1:120, > column_2 = structure(c( > 1,2,3,4,5,6,7,8, > 1,2,3,4,5,6,7,8, > 1,2,3,4,5,6,7,8, > 1,2,3,4,5,6,7,8, > 1,2,3,4,5,6,7,8, > 1,2,3,4,5,6,7,8, > 1,2,3,4,5,6,7,8, > 1,2,3,4,5,6,7,8, > 1,2,3,4,5,6,7,8, > 1,2,3,4,5,6,7,8, > 1,2,3,4,5,6,7,8, > 1,2,3,4,5,6,7,8, > 1,2,3,4,5,6,7,8, > 1,2,3,4,5,6,7,8, > 1,2,3,4,5,6,7,8), .Label = c("Unst.", "ESAT6", "CFP10", "Rv3615c", > "Rv2654", "Rv3879", "Rv3873", "PHA"), class = "factor"), > column_3 = structure(c( > 0,0,0,0,0,0,0,0, > 0,0,0,0,0,0,0,0, > 0,0,0,0,0,0,0,0, > 0,0,0,0,0,0,0,0, > 0,0,0,0,0,0,0,0, > 0,0,0,0,0,0,0,0, > 0,0,0,0,0,0,0,0, > 1,1,1,1,1,1,1,1, > 1,1,1,1,1,1,1,1, > 1,1,1,1,1,1,1,1, > 1,1,1,1,1,1,1,1, > 1,1,1,1,1,1,1,1, > 1,1,1,1,1,1,1,1, > 1,1,1,1,1,1,1,1, > 0,0,0,0,0,0,0,0)), > column_4 = c( > > 192.0519108,183.6403531,53.46798757,83.60638077,69.60749873,159.4706861,256.8765622,499.2899303, > > 2170.799076,1411.349719,2759.472348,2098.973397,2164.739515,1288.676574,1611.486543,6205.229575, > > 870.7424981,465.9967135,191.8962375,864.0937485,2962.693675,1289.259137,2418.651212,7345.712517, > 0,168.1198893,674.4342961,101.1575401,47.81596237,0,0,1420.793922, > > 142.6871331,5.466468742,291.9564635,80.73914133,73.02239621,64.47806871,144.3543635,3167.959757, > > 3164.748333,1092.634557,28733.20269,1207.87783,729.6090973,151.8706088,241.2466141,9600.963594, > > 1411.718287,12569.96285,1143.254476,6317.378481,16542.27718,79.68025792,1958.495138,7224.503437, > > 208.4382941,69.48609769,656.691151,0.499017582,7114.910926,187.6296174,41.73980805,8930.784541, > > 4.276752185,0.432300363,60.89228665,1.103924786,0.490686366,1.812993239,7.264531581,1518.610307, > > 2172.051528,595.8513744,17141.84336,589.6565971,1340.287628,117.350942,593.7034054,24043.61463, > > 0,81.83292179,1539.864321,36.41722958,8.385131047,161.7647376,65.21615696,7265.573875, > > 97.84753179,154.051827,0.613835842,10.06138851,45.04879285,176.8284258,18795.75462,30676.769, > > 5780.34957,944.2200834,2398.235596,1083.393165,2541.714557,1251.670895,1547.178549,1792.679176, > > 3067.988416,8117.210173,23676.02226,8251.937547,17360.80494,18563.61561,16941.865,31453.96708, > > 2767.493803,4796.33016,12292.93705,3864.657567,9380.673835,14886.44683,8457.88646,26050.47191)), > .Names = c("row", "stimulation", "positivity", "copy"), row.names = > c(NA, -120L), > class = "data.frame") > > key.plot<-list( > space="top", columns=2, > text=list(c("Positive", "Negative"), col="black"), > points=list(pch=c(16,1), col="black")) > > datmeA <- aggregate(copy ~ positivity+stimulation, my.data, median, na.rm = T) > > X<-c(0.7, 1.3, 1.7, 2.3) > > Y<-max(copy) > > stripplot( > copy ~ factor(positivity)|factor(stimulation, levels = c("Unst.", > "ESAT6","CFP10","Rv3615c", "Rv2654","Rv3879", "Rv3873","PHA")), > my.data, > group = positivity, > hor=F, > layout = c(8,1), > scales = list(x = list(at = c(1,2), labels = c("N","P"))), > jitter.data=TRUE, pch=c(16,1), col="black", > ylab=expression(bold("Copy")), > xlab=expression(bold("Stimulation")), > main="Plot", > par.settings = list(strip.background=list(col="white")), > par.strip.text=list(font=2), > key = key.plot, > panel = function(x, y, ...) > { > pnl = panel.number() > k<-0 > for (i in 1:2){ > datme<-subset(datmeA, positivity==i-1) > w<-i+k > panel.segments(x0 = X[w], y0 = datme[datme[,2]== > levels(datme[,2])[pnl],"copy"], > x1 = X[w+1], y1 = datme[datme[,2]== > levels(datme[,2])[pnl],"copy"],lwd = 2, col = "black") > k=k+1 > > panel.stripplot(x,y, ...) > } > } > ) > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
