Related
I am plotting correlation coefficients (values = 0.0:1.0) for two isotopes measured in each individual from two populations. I would like to have a fixed aspect-ratio for my scatter-plot so that the x- and y-axis are exactly the same size no matter the graphics device. Suggestions?
This is my first plot in R, any comments on refinements to my code is appreciated? Finally, is it worth investing in learning the basic plotting techniques or should I jump right to ggplot2 or lattice?
My plot script:
## Create dataset
WW_corr <-
structure(list(South_N15 = c(0.7976495, 0.1796725, 0.5338347,
0.4103769, 0.7447027, 0.5080296, 0.7566544, 0.7432026, 0.8927161
), South_C13 = c(0.76706752, 0.02320767, 0.88429902, 0.36648357,
0.73840937, 0.0523504, 0.52145159, 0.50707858, 0.51874445), North_N15 = c(0.7483608,
0.4294148, 0.9283554, 0.8831571, 0.5056481, 0.1945943, 0.8492716,
0.5759033, 0.7483608), North_C13 = c(0.08114805, 0.47268136,
0.94975596, 0.06023815, 0.33652839, 0.53055943, 0.30228833, 0.8864435,
0.08114805)), .Names = c("South_N15", "South_C13", "North_N15",
"North_C13"), row.names = c(NA, -9L), class = "data.frame")
opar <- par()
## Plot results
par(oma = c(1, 0, 0, 0), mar = c(4, 5, 2, 2))
plot(1,1,xlim=c(0:1.0), ylim=c(0:1.0), type="n", las=1, bty="n", main = NULL,
ylab=expression(paste("Correlation Coefficient (r) for ", delta ^{15},"N ",
"\u0028","\u2030","\u0029")),
xlab=expression(paste("Correlation Coefficient (r) for ", delta ^{13},"C ",
"\u0028","\u2030","\u0029")))
points(WW_corr$South_N15, WW_corr$South_C13, pch = 23, cex = 1.25,
bg ="antiquewhite4", col = "antiquewhite4")
points(WW_corr$North_N15, WW_corr$North_C13, pch = 15, cex = 1.25,
bg ="black")
axis(1, at = seq(0, 1.0, by = 0.1), labels = F, tick = TRUE, tck = -0.01)
axis(2, at = seq(0, 1.0, by = 0.1), labels = F, tick = TRUE, tck = -0.01)
abline(h=.86, v=.86, col = "gray60", lty = 2)
legend("topleft", c("North", "South"), pch = c(15, 23),
col = c("black", "antiquewhite4"), pt.bg = c("black", "antiquewhite4"),
horiz=TRUE, bty = "n")
par(opar)
par(pty="s")
plot(...)
sets the plot type to be square, which will do the job (I think) in your case because your x and y ranges are the same. Fairly well hidden option documented in ?par.
Using asp=1 as a parameter to plot will get interpreted by the low-level plot.window call and should give you a unitary aspect ratio. There is the potential that a call using ylim and xlim could conflict with an aspect ratio scpecification and the asp should "prevail". That's a very impressive first R graph, by the away. And an excellent question construction. High marks.
The one jarring note was your use of the construction xlim=c(0:1.0). Since xlim expects a two element vector, I would have expected xlim=c(0,1). Fewer keystrokes and less subject to error in the future if you changed to a different set of limits, since the ":" operator would give you unexpected results if you tried that with "0:2.5".
I am plotting correlation coefficients (values = 0.0:1.0) for two isotopes measured in each individual from two populations. I would like to have a fixed aspect-ratio for my scatter-plot so that the x- and y-axis are exactly the same size no matter the graphics device. Suggestions?
This is my first plot in R, any comments on refinements to my code is appreciated? Finally, is it worth investing in learning the basic plotting techniques or should I jump right to ggplot2 or lattice?
My plot script:
## Create dataset
WW_corr <-
structure(list(South_N15 = c(0.7976495, 0.1796725, 0.5338347,
0.4103769, 0.7447027, 0.5080296, 0.7566544, 0.7432026, 0.8927161
), South_C13 = c(0.76706752, 0.02320767, 0.88429902, 0.36648357,
0.73840937, 0.0523504, 0.52145159, 0.50707858, 0.51874445), North_N15 = c(0.7483608,
0.4294148, 0.9283554, 0.8831571, 0.5056481, 0.1945943, 0.8492716,
0.5759033, 0.7483608), North_C13 = c(0.08114805, 0.47268136,
0.94975596, 0.06023815, 0.33652839, 0.53055943, 0.30228833, 0.8864435,
0.08114805)), .Names = c("South_N15", "South_C13", "North_N15",
"North_C13"), row.names = c(NA, -9L), class = "data.frame")
opar <- par()
## Plot results
par(oma = c(1, 0, 0, 0), mar = c(4, 5, 2, 2))
plot(1,1,xlim=c(0:1.0), ylim=c(0:1.0), type="n", las=1, bty="n", main = NULL,
ylab=expression(paste("Correlation Coefficient (r) for ", delta ^{15},"N ",
"\u0028","\u2030","\u0029")),
xlab=expression(paste("Correlation Coefficient (r) for ", delta ^{13},"C ",
"\u0028","\u2030","\u0029")))
points(WW_corr$South_N15, WW_corr$South_C13, pch = 23, cex = 1.25,
bg ="antiquewhite4", col = "antiquewhite4")
points(WW_corr$North_N15, WW_corr$North_C13, pch = 15, cex = 1.25,
bg ="black")
axis(1, at = seq(0, 1.0, by = 0.1), labels = F, tick = TRUE, tck = -0.01)
axis(2, at = seq(0, 1.0, by = 0.1), labels = F, tick = TRUE, tck = -0.01)
abline(h=.86, v=.86, col = "gray60", lty = 2)
legend("topleft", c("North", "South"), pch = c(15, 23),
col = c("black", "antiquewhite4"), pt.bg = c("black", "antiquewhite4"),
horiz=TRUE, bty = "n")
par(opar)
par(pty="s")
plot(...)
sets the plot type to be square, which will do the job (I think) in your case because your x and y ranges are the same. Fairly well hidden option documented in ?par.
Using asp=1 as a parameter to plot will get interpreted by the low-level plot.window call and should give you a unitary aspect ratio. There is the potential that a call using ylim and xlim could conflict with an aspect ratio scpecification and the asp should "prevail". That's a very impressive first R graph, by the away. And an excellent question construction. High marks.
The one jarring note was your use of the construction xlim=c(0:1.0). Since xlim expects a two element vector, I would have expected xlim=c(0,1). Fewer keystrokes and less subject to error in the future if you changed to a different set of limits, since the ":" operator would give you unexpected results if you tried that with "0:2.5".
I am plotting correlation coefficients (values = 0.0:1.0) for two isotopes measured in each individual from two populations. I would like to have a fixed aspect-ratio for my scatter-plot so that the x- and y-axis are exactly the same size no matter the graphics device. Suggestions?
This is my first plot in R, any comments on refinements to my code is appreciated? Finally, is it worth investing in learning the basic plotting techniques or should I jump right to ggplot2 or lattice?
My plot script:
## Create dataset
WW_corr <-
structure(list(South_N15 = c(0.7976495, 0.1796725, 0.5338347,
0.4103769, 0.7447027, 0.5080296, 0.7566544, 0.7432026, 0.8927161
), South_C13 = c(0.76706752, 0.02320767, 0.88429902, 0.36648357,
0.73840937, 0.0523504, 0.52145159, 0.50707858, 0.51874445), North_N15 = c(0.7483608,
0.4294148, 0.9283554, 0.8831571, 0.5056481, 0.1945943, 0.8492716,
0.5759033, 0.7483608), North_C13 = c(0.08114805, 0.47268136,
0.94975596, 0.06023815, 0.33652839, 0.53055943, 0.30228833, 0.8864435,
0.08114805)), .Names = c("South_N15", "South_C13", "North_N15",
"North_C13"), row.names = c(NA, -9L), class = "data.frame")
opar <- par()
## Plot results
par(oma = c(1, 0, 0, 0), mar = c(4, 5, 2, 2))
plot(1,1,xlim=c(0:1.0), ylim=c(0:1.0), type="n", las=1, bty="n", main = NULL,
ylab=expression(paste("Correlation Coefficient (r) for ", delta ^{15},"N ",
"\u0028","\u2030","\u0029")),
xlab=expression(paste("Correlation Coefficient (r) for ", delta ^{13},"C ",
"\u0028","\u2030","\u0029")))
points(WW_corr$South_N15, WW_corr$South_C13, pch = 23, cex = 1.25,
bg ="antiquewhite4", col = "antiquewhite4")
points(WW_corr$North_N15, WW_corr$North_C13, pch = 15, cex = 1.25,
bg ="black")
axis(1, at = seq(0, 1.0, by = 0.1), labels = F, tick = TRUE, tck = -0.01)
axis(2, at = seq(0, 1.0, by = 0.1), labels = F, tick = TRUE, tck = -0.01)
abline(h=.86, v=.86, col = "gray60", lty = 2)
legend("topleft", c("North", "South"), pch = c(15, 23),
col = c("black", "antiquewhite4"), pt.bg = c("black", "antiquewhite4"),
horiz=TRUE, bty = "n")
par(opar)
par(pty="s")
plot(...)
sets the plot type to be square, which will do the job (I think) in your case because your x and y ranges are the same. Fairly well hidden option documented in ?par.
Using asp=1 as a parameter to plot will get interpreted by the low-level plot.window call and should give you a unitary aspect ratio. There is the potential that a call using ylim and xlim could conflict with an aspect ratio scpecification and the asp should "prevail". That's a very impressive first R graph, by the away. And an excellent question construction. High marks.
The one jarring note was your use of the construction xlim=c(0:1.0). Since xlim expects a two element vector, I would have expected xlim=c(0,1). Fewer keystrokes and less subject to error in the future if you changed to a different set of limits, since the ":" operator would give you unexpected results if you tried that with "0:2.5".
My problem concerns the making of a graph for a publication in R. I have used the plot function like follows:
plot(x=data$SL, y=data$BD, xlab = "SL (mm)", ylab = "BD (mm)", pch=data$pch)
SL ranges from 51.7 to 73.7 and BD from 13.5 to 20.4. Unfortunately I am not allowed to post images yet.
However, wanting to get rid of the box I used "axes=F". Problem now is lack of control over the axis function. I used:
axis(side=1, lwd=3, xpd=TRUE, at=c(min(data$SL):max(data$SL)))
axis(side=2, lwd=3, xpd=TRUE, at=c(min(data$BD):max(data$BD)))
Problem is that I can't manage to get the y- and x-axis to come together on the same point as in the plot with the box. How to let the x- and y- axis to touch each other?
Most likely setting xaxs = "i" and yaxs = "i" will help you getting the desired behaviour.
plot(c(1,2,3),c(2,4,6),axes=F,xaxs = "i",yaxs="i",xlim=c(0,3),ylim=c(0,6))
axis(side=1, lwd=3, xpd=TRUE, at=0:3)
axis(side=2, lwd=3, xpd=TRUE, at=seq(0,6,2))
Try box(bty='L') to draw only the left and bottom parts of the box. You could also just draw the lines yourself using lines, segments, or abline and using grconvertX and grconvertY functions to find the locations where to draw the lines.
I suggest that you follow the procedure you outlined and then use:
box(which = "plot", bty = "l")
e.g.:
plot.new()
plot.window(xlim = c(1, 18), ylim = c(2, 20))
points(1:18, 2:19, pch = 1, col = "#FF7F24", cex = 1.2)
lines(1:18, 2:19, col = "#FF7F24", lwd = 2)
axis(side = 1,
lwd = 0,
lwd.ticks = 1,
at = 1:18,
cex.axis = 0.9)
title(main = "Plot",
ylab = "Y-Axis")
legend("top",
legend = c("Legend"),
col = c("#FF7F24"),
text.col = c("#FF7F24"),
pch = 1,
bty = "n",
cex = 1.2)
axis(side = 2,
lwd = 0,
lwd.ticks = 1)
box(which = "plot", bty = "l")
You should pass the options lwd = 0 and lwd.ticks = 1 to your seperate axis() calls in order to prevent some parts of your axes to appear fatter than other parts of your axis because some get overlayed by your call to box() and some do not.
The solution of using box() at the end is, I think, more general in that you can use it when e.g. you cannot or do not want to pass bty = "l" in your plot.default or plot.window call.
I am plotting correlation coefficients (values = 0.0:1.0) for two isotopes measured in each individual from two populations. I would like to have a fixed aspect-ratio for my scatter-plot so that the x- and y-axis are exactly the same size no matter the graphics device. Suggestions?
This is my first plot in R, any comments on refinements to my code is appreciated? Finally, is it worth investing in learning the basic plotting techniques or should I jump right to ggplot2 or lattice?
My plot script:
## Create dataset
WW_corr <-
structure(list(South_N15 = c(0.7976495, 0.1796725, 0.5338347,
0.4103769, 0.7447027, 0.5080296, 0.7566544, 0.7432026, 0.8927161
), South_C13 = c(0.76706752, 0.02320767, 0.88429902, 0.36648357,
0.73840937, 0.0523504, 0.52145159, 0.50707858, 0.51874445), North_N15 = c(0.7483608,
0.4294148, 0.9283554, 0.8831571, 0.5056481, 0.1945943, 0.8492716,
0.5759033, 0.7483608), North_C13 = c(0.08114805, 0.47268136,
0.94975596, 0.06023815, 0.33652839, 0.53055943, 0.30228833, 0.8864435,
0.08114805)), .Names = c("South_N15", "South_C13", "North_N15",
"North_C13"), row.names = c(NA, -9L), class = "data.frame")
opar <- par()
## Plot results
par(oma = c(1, 0, 0, 0), mar = c(4, 5, 2, 2))
plot(1,1,xlim=c(0:1.0), ylim=c(0:1.0), type="n", las=1, bty="n", main = NULL,
ylab=expression(paste("Correlation Coefficient (r) for ", delta ^{15},"N ",
"\u0028","\u2030","\u0029")),
xlab=expression(paste("Correlation Coefficient (r) for ", delta ^{13},"C ",
"\u0028","\u2030","\u0029")))
points(WW_corr$South_N15, WW_corr$South_C13, pch = 23, cex = 1.25,
bg ="antiquewhite4", col = "antiquewhite4")
points(WW_corr$North_N15, WW_corr$North_C13, pch = 15, cex = 1.25,
bg ="black")
axis(1, at = seq(0, 1.0, by = 0.1), labels = F, tick = TRUE, tck = -0.01)
axis(2, at = seq(0, 1.0, by = 0.1), labels = F, tick = TRUE, tck = -0.01)
abline(h=.86, v=.86, col = "gray60", lty = 2)
legend("topleft", c("North", "South"), pch = c(15, 23),
col = c("black", "antiquewhite4"), pt.bg = c("black", "antiquewhite4"),
horiz=TRUE, bty = "n")
par(opar)
par(pty="s")
plot(...)
sets the plot type to be square, which will do the job (I think) in your case because your x and y ranges are the same. Fairly well hidden option documented in ?par.
Using asp=1 as a parameter to plot will get interpreted by the low-level plot.window call and should give you a unitary aspect ratio. There is the potential that a call using ylim and xlim could conflict with an aspect ratio scpecification and the asp should "prevail". That's a very impressive first R graph, by the away. And an excellent question construction. High marks.
The one jarring note was your use of the construction xlim=c(0:1.0). Since xlim expects a two element vector, I would have expected xlim=c(0,1). Fewer keystrokes and less subject to error in the future if you changed to a different set of limits, since the ":" operator would give you unexpected results if you tried that with "0:2.5".