Re: [R] add outer strip for levels in lattice plot (useOuterStrips alternative for Lattice)
Dear Duncan, I tried the solution you indicated in the previous message but I am still obtaining the error length(dimx) == 2 is not TRUE. Assuming that the dataframe is working (it does work on my machine), I added the useOuterStrips bit as you showed: useOuterStrips( strip = strip.custom( factor.levels = paste(column,1:6), par.strip.text = list(cex = 0.75)), strip.left = strip.custom(factor.levels = paste(row, 1:2), horizontal = FALSE, par.strip.text = list(cex = 0.75) ), xyplot(Rn ~ Cycle | Well, data = my.data, groups = Well, ylab= Y axis, xlab=X axis, main=Title, scales = list( x = list(draw = FALSE), y = list(draw = FALSE), relation=same ), as.table = TRUE, layout = L, par.settings = list( strip.background=list(col=white), axis.text = list(cex = 0.6), par.xlab.text = list(cex = 0.75), par.ylab.text = list(cex = 0.75), par.main.text = list(cex = 0.8), superpose.symbol = list(pch = ., cex = 1) ), strip= FALSE, type = l, col = 3, panel = panel.superpose ) ) WHere am I getting it wrong? Best regards Luigi On Thu, Jul 9, 2015 at 11:36 AM, Duncan Mackay dulca...@bigpond.com wrote: Hi Luigi If you wanted to add some text you could use grid.text from the grid package I use it regularly for annotating See also https://stat.ethz.ch/pipermail/r-help/2005-February/066264.html https://stat.ethz.ch/pipermail/r-help/2005-April/069456.html Duncan -Original Message- From: Luigi Marongiu [mailto:marongiu.lu...@gmail.com] Sent: Thursday, 9 July 2015 19:01 To: Duncan Mackay Subject: Re: [R] add outer strip for levels in lattice plot (useOuterStrips alternative for Lattice) Dear Duncan, funny this deviation of the variables outcomes. yesterday when i wrote the script it worked fine and even today when i loaded it on rstudio at work i obtained: Cycle num[1:540] Linenum[1:540] Rn num[1:540] Target chr[1:540] Wellnum[1:540] my.data 540 obs. of 4 variables and the call for my.data returned a proper dataframe. I did not write lattice_Extra but latticeextra's useOuterStrips() [forgot to capitalize the second E]. I'll try your suggestion, but essentially wouldn't be possible to write some text on the top and left portions of the xyplot graph using some text function within lattice itself without having to call latticeExtra? Many thanks regards Luigi On Thu, Jul 9, 2015 at 3:56 AM, Duncan Mackay dulca...@bigpond.com wrote: Hi Luigi str(my.data) 'data.frame': 540 obs. of 4 variables: $ Line : chr 1 2 3 4 ... $ Well : chr 1 1 1 1 ... $ Target: chr alpha alpha alpha alpha ... $ Rn: chr 0.728 0.735 0.749 0.758 ... You didnot create the data.frame properly mydata - data.frame(Line=Line, Well=Well, Target=Target, Rn=Rn,Cycle= Cycle) str(mydata) 'data.frame': 540 obs. of 4 variables: $ Line : num 1 2 3 4 5 6 7 8 9 10 ... $ Well : num 1 1 1 1 1 1 1 1 1 1 ... $ Target: chr alpha alpha alpha alpha ... $ Rn: num 0.728 0.735 0.749 0.758 0.77 0.778 0.78 0.784 0.786 0.785 ... I was having problems with your script so I started with the basics (before I found the problem with the df) xyplot(Rn ~ Cycle | sprintf(%2d,Well), data = mydata, as.table = TRUE, layout = c(6,2), groups = Well) You are not splitting up the data with groups being the same as the conditioning. It can be necessary to use this setup in some cases but not this. latticeExtra is on Cran so you can use install.packages(latticeExtra) or use the menu I have never heard of lattice_Extra mydata$rown - ifelse(mydata$Well6,2,1) mydata$welln - rep(1:6, 2)[sapply(mydata$Well, pmatch, 1:12)] useOuterStrips(strip = strip.custom(factor.levels = paste(column,1:6), par.strip.text = list(cex = 0.75)), strip.left = strip.custom(factor.levels = paste(row, 1:2), horizontal = FALSE, par.strip.text = list(cex = 0.75)), xyplot(Rn ~ Cycle | welln*rown, data = mydata, as.table = TRUE, layout = c(6,2) ) ) ## useOuterStrips ps.Colours - c(#00,#FF,#00FF00,#FF,#FFA54F, #00,#FF00FF,#C0,#00B414,#FFD18F, #00B2EE,#ffe5cc,#6A5ACD,#C0C0C0,#CC, #6495ED,#FFFAFA) useOuterStrips(strip = strip.custom(factor.levels = paste(column,1:6), par.strip.text = list(cex = 0.75)), strip.left = strip.custom(factor.levels = paste(row, 1:2), horizontal = FALSE
Re: [R] add outer strip for levels in lattice plot (useOuterStrips alternative for Lattice)
Hi Luigi str(my.data) 'data.frame': 540 obs. of 4 variables: $ Line : chr 1 2 3 4 ... $ Well : chr 1 1 1 1 ... $ Target: chr alpha alpha alpha alpha ... $ Rn: chr 0.728 0.735 0.749 0.758 ... You didnot create the data.frame properly mydata - data.frame(Line=Line, Well=Well, Target=Target, Rn=Rn,Cycle= Cycle) str(mydata) 'data.frame': 540 obs. of 4 variables: $ Line : num 1 2 3 4 5 6 7 8 9 10 ... $ Well : num 1 1 1 1 1 1 1 1 1 1 ... $ Target: chr alpha alpha alpha alpha ... $ Rn: num 0.728 0.735 0.749 0.758 0.77 0.778 0.78 0.784 0.786 0.785 ... I was having problems with your script so I started with the basics (before I found the problem with the df) xyplot(Rn ~ Cycle | sprintf(%2d,Well), data = mydata, as.table = TRUE, layout = c(6,2), groups = Well) You are not splitting up the data with groups being the same as the conditioning. It can be necessary to use this setup in some cases but not this. latticeExtra is on Cran so you can use install.packages(latticeExtra) or use the menu I have never heard of lattice_Extra mydata$rown - ifelse(mydata$Well6,2,1) mydata$welln - rep(1:6, 2)[sapply(mydata$Well, pmatch, 1:12)] useOuterStrips(strip = strip.custom(factor.levels = paste(column,1:6), par.strip.text = list(cex = 0.75)), strip.left = strip.custom(factor.levels = paste(row, 1:2), horizontal = FALSE, par.strip.text = list(cex = 0.75)), xyplot(Rn ~ Cycle | welln*rown, data = mydata, as.table = TRUE, layout = c(6,2) ) ) ## useOuterStrips ps.Colours - c(#00,#FF,#00FF00,#FF,#FFA54F, #00,#FF00FF,#C0,#00B414,#FFD18F, #00B2EE,#ffe5cc,#6A5ACD,#C0C0C0,#CC, #6495ED,#FFFAFA) useOuterStrips(strip = strip.custom(factor.levels = paste(column,1:6), par.strip.text = list(cex = 0.75)), strip.left = strip.custom(factor.levels = paste(row, 1:2), horizontal = FALSE, par.strip.text = list(cex = 0.75)), xyplot(Rn ~ Cycle | welln*rown, data = mydata, as.table = TRUE, groups = Well, col = ps.Colours, layout = c(6,2) ) ) ## useOuterStrips Duncan -Original Message- From: Luigi Marongiu [mailto:marongiu.lu...@gmail.com] Sent: Thursday, 9 July 2015 09:22 To: Duncan Mackay; Dennis Murphy; r-help Subject: Re: [R] add outer strip for levels in lattice plot (useOuterStrips alternative for Lattice) In relation to this question I have prepared a workable example. First I prepare a dataframe with three variables (Cycle, Target, Rn), then I plot the results with lattice's xyplot(). I won't use the scales but only the labels and the panels are NOT indicated by the variable Well. What I would need to use are instead the vectors row.name and col.name that can identify each column and row of the plot. Secondly I create replicates of the row.name and col.name in order to fit the data and create a second dataframe, then I plot using lattice extra's useOuterStrips(). However (a) I think the call is wrong anyway, (b) I obtain Error: length(dimx) == 2 is not TRUE (c) I need a package on top of lattice (d) I might introduce errors during the creation of the second dataframe. The requirements remains to create a strip on the top and left side of the plot to allocate the elements of row.name and col.name possibly using lattice only. Thank you for your help. Luigi Line-c(1,2,3,4,5,6,7,8,9,10, 11,12,13,14,15,16,17,18,19,20, 21,22,23,24,25,26,27,28,29,30, 31,32,33,34,35,36,37,38,39,40, 41,42,43,44,45,46,47,48,49,50, 51,52,53,54,55,56,57,58,59,60, 61,62,63,64,65,66,67,68,69,70, 71,72,73,74,75,76,77,78,79,80, 81,82,83,84,85,86,87,88,89,90, 91,92,93,94,95,96,97,98,99,100, 101,102,103,104,105,106,107,108,109, 110,111,112,113,114,115,116,117,118, 119,120,121,122,123,124,125,126,127, 128,129,130,131,132,133,134,135, 136,137,138,139,140,141,142,143,144, 145,146,147,148,149,150,151,152,153, 154,155,156,157,158,159,160,161,162, 163,164,165,166,167,168,169,170, 171,172,173,174,175,176,177,178,179
Re: [R] add outer strip for levels in lattice plot (useOuterStrips alternative for Lattice)
,1.241,1.234,1.228, 1.222,1.216,1.213,1.208,1.205,1.2,1.197, 1.192,1.189,1.186,1.184,1.182,1.181,1.178, 1.178,0.802,0.801,0.801,0.8,0.799,0.797, 0.794,0.791,0.785,0.781,0.777,0.772,0.766, 0.76,0.756,0.753,0.751,0.746,0.742,0.739, 0.735,0.732,0.728,0.726,0.725,0.722,0.718, 0.717,0.716,0.715,0.71,0.709,0.711,0.71, 0.709,0.709,0.709,0.709,0.708,0.709,0.71, 0.71,0.711,0.711,0.712,1.209,1.206,1.204, 1.202,1.197,1.186,1.175,1.165,1.154,1.143, 1.133,1.12,1.11,1.105,1.098,1.091,1.085, 1.078,1.072,1.067,1.063,1.054,1.049,1.048, 1.04,1.036,1.033,1.029,1.027,1.024,1.021, 1.019,1.017,1.013,1.01,1.008,1.006,1.005, 1.004,1.002,1.002,1.001,1,0.998,0.995, 2.936,2.942,2.946,2.951,2.956,2.956,2.968, 2.964,2.953,2.945,2.939,2.929,2.919,2.909, 2.902,2.893,2.882,2.871,2.857,2.847,2.835, 2.825,2.819,2.806,2.795,2.787,2.781,2.766, 2.761,2.752,2.749,2.74,2.731,2.722,2.718, 2.711,2.705,2.7,2.693,2.69,2.686,2.676, 2.672,2.668,2.667,1.032,1.033,1.031,1.033, 1.031,1.029,1.025,1.02,1.019,1.016,1.012, 1.008,1.007,1.011,1.015,1.032,1.068,1.124, 1.209,1.327,1.472,1.632,1.8,1.971,2.14, 2.302,2.459,2.612,2.754,2.886,3.008,3.122, 3.218,3.306,3.39,3.472,3.547,3.613,3.674, 3.731,3.772,3.81,3.84,3.86,3.882,0.808, 0.808,0.808,0.807,0.805,0.804,0.802,0.801, 0.798,0.796,0.794,0.79,0.788,0.785,0.781, 0.78,0.777,0.774,0.772,0.771,0.769,0.767, 0.767,0.766,0.766,0.764,0.764,0.765,0.762, 0.762,0.76,0.759,0.759,0.758,0.758,0.758, 0.756,0.754,0.754,0.753,0.754,0.755,0.753, 0.754,0.753) my.data - as.data.frame(cbind(Line, Well, Target, Rn)) L - c(6,2) row.name - c(A, B) col.name - 1:6 library(lattice) xyplot(Rn ~ Cycle | Well, data = my.data, groups = Well, ylab= Y axis, xlab=X axis, main=Title, scales = list( x = list(draw = FALSE), y = list(draw = FALSE), relation=same ), as.table = TRUE, layout = L, par.settings = list( strip.background=list(col=white), axis.text = list(cex = 0.6), par.xlab.text = list(cex = 0.75), par.ylab.text = list(cex = 0.75), par.main.text = list(cex = 0.8), superpose.symbol = list(pch = ., cex = 1) ), strip= FALSE, type = l, col = 3, panel = panel.superpose ) ROW - c(rep(row.name[1], 45*6), rep(row.name[2], 45*6)) CO - c(rep(col.name[1], 45), rep(col.name[2], 45), rep(col.name[3], 45), rep(col.name[4], 45), rep(col.name[5], 45), rep(col.name[6], 45) ) COL - rep(CO,2) new.data - cbind(my.data, ROW, COL) head(new.data, 200) useOuterStrips( xyplot(Rn ~ Cycle | Well, data = my.data, groups = Well, ylab= Y axis, xlab=X axis, main=Title, scales = list( x = list(draw = FALSE), y = list(draw = FALSE), relation=same ), as.table = TRUE, layout = L, par.settings = list( strip.background=list(col=white), axis.text = list(cex = 0.6), par.xlab.text = list(cex = 0.75), par.ylab.text = list(cex = 0.75), par.main.text = list(cex = 0.8), superpose.symbol = list(pch = ., cex = 1) ), strip= FALSE, type = l, col = 3, panel = panel.superpose ), c(ROW,COL)) On Tue, Jul 7, 2015 at 12:19 AM, Duncan Mackay dulca...@bigpond.com wrote: Hi Luigi Not exactly sure what you want Have a look at https://stat.ethz.ch/pipermail/r-help/2007-May/132785.html and https://stat.ethz.ch/pipermail/r-help/2007-July/135551.html otherwise have a look at ?trellis.focus and https://stat.ethz.ch/pipermail/r-help/2006-July/109585.html failing that ?gridRect and ?gridText from library(grid) Regards Duncan Duncan Mackay Department of Agronomy and Soil Science University of New England Armidale NSW 2351 Email: home: mac...@northnet.com.au -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Luigi Marongiu Sent: Monday, 6 July 2015 09:56 To: r-help Subject: [R] add outer strip for levels in lattice plot (useOuterStrips alternative for Lattice
Re: [R] add outer strip for levels in lattice plot (useOuterStrips alternative for Lattice)
Hi Luigi Not exactly sure what you want Have a look at https://stat.ethz.ch/pipermail/r-help/2007-May/132785.html and https://stat.ethz.ch/pipermail/r-help/2007-July/135551.html otherwise have a look at ?trellis.focus and https://stat.ethz.ch/pipermail/r-help/2006-July/109585.html failing that ?gridRect and ?gridText from library(grid) Regards Duncan Duncan Mackay Department of Agronomy and Soil Science University of New England Armidale NSW 2351 Email: home: mac...@northnet.com.au -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Luigi Marongiu Sent: Monday, 6 July 2015 09:56 To: r-help Subject: [R] add outer strip for levels in lattice plot (useOuterStrips alternative for Lattice) Dear all, I would like to add an outer strip or something like that on a lattice plot I am making. Such plot contains 384 cells and, since I am not interested in the axis values, I set: scales = list( x = list(draw = FALSE), y = list(draw = FALSE), relation=same ), on a xyplot from the LATTICE package. Nevertheless there are axis labels which run like: ylab= Y axis, xlab= X axis, I would like to place some more information regarding the individual cells thus I would like to draw a sort of extra axis labels that are similar to the outer strip of the LATTICE_EXTRA package, that is markers placed between the axis labels and the axis values and centered for each cells, typically placed on the top and left sides of the plot. This is performed by the useOuterStrips function but: a) LatticeExtra is not in the CRAN repository thus I have to install it through a more laborious approach which makes LatticeExtra less direct than Lattice b) useOuterStrips uses information directly from the data whereas I will have to provide the extra information from ad hoc vectors not present in the data set. The question therefore is: is there a way to write text from a vector in the top and left corners of a lattice xyplot and place the individual elements at the centre of the rows and columns that compose the graph? Many thanks, Luigi __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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 -- To UNSUBSCRIBE and more, see 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] add outer strip for levels in lattice plot (useOuterStrips alternative for Lattice)
Dear all, I would like to add an outer strip or something like that on a lattice plot I am making. Such plot contains 384 cells and, since I am not interested in the axis values, I set: scales = list( x = list(draw = FALSE), y = list(draw = FALSE), relation=same ), on a xyplot from the LATTICE package. Nevertheless there are axis labels which run like: ylab= Y axis, xlab= X axis, I would like to place some more information regarding the individual cells thus I would like to draw a sort of extra axis labels that are similar to the outer strip of the LATTICE_EXTRA package, that is markers placed between the axis labels and the axis values and centered for each cells, typically placed on the top and left sides of the plot. This is performed by the useOuterStrips function but: a) LatticeExtra is not in the CRAN repository thus I have to install it through a more laborious approach which makes LatticeExtra less direct than Lattice b) useOuterStrips uses information directly from the data whereas I will have to provide the extra information from ad hoc vectors not present in the data set. The question therefore is: is there a way to write text from a vector in the top and left corners of a lattice xyplot and place the individual elements at the centre of the rows and columns that compose the graph? Many thanks, Luigi __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
