Hi, Can the boxplot design illustrated in the post (http://stackoverflow.com/questions/39849459/how-to-create-boxplots-with-a-continuous-x-axis-in-r) be reproduced with lattice or a lattice-derived function? Thank you Sebastien
Vertical boxplot with a continuous X axis
5 messages · Richard M. Heiberger, Bert Gunter, Sebastien Bihorel
Yes, this is exactly what the panel function
panel.bwplot.intermediate.hh
along with the
position()
function in the HH package was designed for.
Continuing with the example in the linked stackoverflow
df <- structure(list(X1 = c(67.0785968921204, 45.5968692796599,
36.9528452430474,
59.0160838607585, 50.0432724395945, 44.3381091105162, 57.9705240678336,
52.5298724133533, 62.0004216014734, 54.1111551461596), X2 = c(66.4508598009841,
46.9692156851792, 37.1419457255043, 60.0582991817961, 50.7717368681294,
44.6962314013419, 57.5490276313784, 52.6394305113891, 62.9297233041122,
56.8151766642767), X3 = c(66.4517425831512, 46.2946539468733,
36.5946733567535, 59.2477934854157, 49.1558840130484, 44.7507905380111,
59.1132983272444, 53.710627728232, 61.7923277906642, 57.5999862897015
), X4 = c(66.1516449763315, 45.4660590159847, 37.2239262718906,
59.2975530712561, 50.2546321578291, 44.7220452966667, 59.8879656465763,
52.321734919241, 62.0802304973764, 56.6507005349853), X5 = c(66.1810558292955,
46.3301985628267, 36.4487743101244, 60.054119632362, 49.1593136549535,
44.5708909518076, 58.5865142665164, 52.5527273219855, 61.3749185309236,
54.1823379401272), X6 = c(65.9530929286517, 45.5120010675769,
36.7924160587984, 58.9428613519645, 50.3412809263164, 44.9671678827697,
57.8718260182012, 51.8954544252633, 62.0173019998447, 56.3833840769146
), X7 = c(66.3862581408135, 46.5872469340431, 36.7585555977493,
58.1374309578563, 50.3399735165261, 44.5739565876491, 57.5245695195136,
52.7613488669329, 61.2500297922529, 55.9202360622414), X8 = c(67.5577910713347,
46.1891742544371, 36.4689522649804, 59.5271358261971, 49.6776114214636,
44.1995317742719, 58.4881363877987, 52.1946266979144, 62.1149998459759,
55.3748655464147), X9 = c(66.3943390258844, 45.843835703738,
37.3485122393333, 59.8591304277037, 49.387883195468, 44.4283817056918,
58.1874530826789, 53.5091378916001, 62.1187451212786, 55.3632760142297
), X10 = c(66.9748072219828, 46.20735965374, 36.7069272963502,
59.5035069226904, 48.8446530329762, 44.8753686249692, 58.0223695284058,
53.2732448917674, 61.2509571513, 54.9615424261546), age = c(55,
37, 31, 59, 49, 47, 69, 68, 69, 66)), .Names = c("X1", "X2",
"X3", "X4", "X5", "X6", "X7", "X8", "X9", "X10", "age"), row.names =
c("GSM1051533_7800246024_R03C02",
"GSM1051534_7800246024_R04C02", "GSM1051535_7800246024_R05C02",
"GSM1051536_7800246024_R06C02", "GSM1051537_7800246085_R01C01",
"GSM1051538_7800246085_R02C01", "GSM1051539_7800246085_R03C01",
"GSM1051540_7800246085_R04C01", "GSM1051541_7800246085_R05C01",
"GSM1051542_7800246085_R06C01"), class = "data.frame")
## install.packages("HH") ## if necessary
library(HH)
df.melt <- reshape2::melt(df, id.vars=c("age"))
df.melt$age.pos <- factor(df.melt$age)
position(df.melt$age.pos) <- levels(df.melt$age.pos)
## three options of x ticks and color
bwplot(value ~ age.pos, data=df.melt,
horizontal=FALSE,
panel=panel.bwplot.intermediate.hh,
scales=list(
x=list(
at=position(df.melt$age.pos), ## placement of tick labels and marks
limits=c(29, 71), ## x limits
tck=1)), ## draw tick marks
xlab="age",
main=list("value ~ age", cex=1.4))
bwplot(value ~ age.pos, data=df.melt,
horizontal=FALSE,
panel=panel.bwplot.intermediate.hh,
scales=list(
x=list(
## at=position(df.melt$age.pos), ## placement of tick labels and marks
limits=c(29, 71), ## x limits
tck=1)), ## draw tick marks
xlab="age",
main=list("value ~ age", cex=1.4))
bwplot(value ~ age.pos, data=df.melt,
horizontal=FALSE,
panel=panel.bwplot.intermediate.hh,
col="blue", ## constant color
scales=list(
x=list(
## at=position(df.melt$age.pos), ## placement of tick labels and marks
limits=c(29, 71), ## x limits
tck=1)), ## draw tick marks
xlab="age",
main=list("value ~ age", cex=1.4))
On Thu, Feb 23, 2017 at 11:52 PM, Sebastien Bihorel
<sebastien.bihorel at cognigencorp.com> wrote:
Hi, Can the boxplot design illustrated in the post (http://stackoverflow.com/questions/39849459/how-to-create-boxplots-with-a-continuous-x-axis-in-r) be reproduced with lattice or a lattice-derived function? Thank you Sebastien
______________________________________________ R-help at 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.
Sebastien:
The linked post is unclear: two of the rows have the same age, so
should there be 10 boxplots for the 10 rows or 9 for the 9 different
ages? I assumed the latter, as otherwise how could one disciminate
rows with the same age that have overlapping values?
For lattice, I just used age as the group= parameter to group by ages
and used panel.bwplot for the panel.groups function. My "aesthetics"
are different than shown in the linked post, but can be altered in
lattice through the panel.bwplot and par.settings parameters as
described in ?panel.bwplot:
y <- unlist(df[,-11])
age <- rep(df[,"age"],10) ## Could be done programatically
xyplot(y~age, groups = age,
panel = function(...){
panel.abline(h = seq(40,65, by=5),
v = seq(30,70, by =5),
col="lightgray")
panel.superpose(...)
},
panel.groups = function(x,y,...)
panel.bwplot(x,y,horiz=FALSE,fill = "lightgray",
pch = 16, cex=.7,col= "black",box.width = 1.5),
par.settings =list(box.rectangle = list(col="black"))
)
However, note that this too could produce a hopeless mishmosh if the
ages are close together so that the boxplots overlap; or you could end
up getting nearly invisible skinny boxes, as in the plot shown in the
linked post. So on the whole, I think you are better off treating the
ages as a factor and thereby separating them, e.g.
bwplot(y~age, fill = "lightgray", horiz = FALSE,
panel = function(...){
panel.abline(h = seq(40,65, by=5),col="lightgray")
panel.bwplot(...)
},
scales = list(x= list(lab = sort(unique(age)))),
par.settings =list(box.rectangle = list(col="black"))
)
Cheers,
Bert
Bert Gunter
"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Thu, Feb 23, 2017 at 8:52 PM, Sebastien Bihorel
<sebastien.bihorel at cognigencorp.com> wrote:
Hi, Can the boxplot design illustrated in the post (http://stackoverflow.com/questions/39849459/how-to-create-boxplots-with-a-continuous-x-axis-in-r) be reproduced with lattice or a lattice-derived function? Thank you Sebastien
______________________________________________ R-help at 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.
Thanks for your reply
----- Original Message -----
From: "Richard M. Heiberger" <rmh at temple.edu>
To: "Sebastien Bihorel" <sebastien.bihorel at cognigencorp.com>
Cc: "r-help" <r-help at r-project.org>
Sent: Friday, February 24, 2017 1:10:44 AM
Subject: Re: [R] Vertical boxplot with a continuous X axis
Yes, this is exactly what the panel function
panel.bwplot.intermediate.hh
along with the
position()
function in the HH package was designed for.
Continuing with the example in the linked stackoverflow
df <- structure(list(X1 = c(67.0785968921204, 45.5968692796599,
36.9528452430474,
59.0160838607585, 50.0432724395945, 44.3381091105162, 57.9705240678336,
52.5298724133533, 62.0004216014734, 54.1111551461596), X2 = c(66.4508598009841,
46.9692156851792, 37.1419457255043, 60.0582991817961, 50.7717368681294,
44.6962314013419, 57.5490276313784, 52.6394305113891, 62.9297233041122,
56.8151766642767), X3 = c(66.4517425831512, 46.2946539468733,
36.5946733567535, 59.2477934854157, 49.1558840130484, 44.7507905380111,
59.1132983272444, 53.710627728232, 61.7923277906642, 57.5999862897015
), X4 = c(66.1516449763315, 45.4660590159847, 37.2239262718906,
59.2975530712561, 50.2546321578291, 44.7220452966667, 59.8879656465763,
52.321734919241, 62.0802304973764, 56.6507005349853), X5 = c(66.1810558292955,
46.3301985628267, 36.4487743101244, 60.054119632362, 49.1593136549535,
44.5708909518076, 58.5865142665164, 52.5527273219855, 61.3749185309236,
54.1823379401272), X6 = c(65.9530929286517, 45.5120010675769,
36.7924160587984, 58.9428613519645, 50.3412809263164, 44.9671678827697,
57.8718260182012, 51.8954544252633, 62.0173019998447, 56.3833840769146
), X7 = c(66.3862581408135, 46.5872469340431, 36.7585555977493,
58.1374309578563, 50.3399735165261, 44.5739565876491, 57.5245695195136,
52.7613488669329, 61.2500297922529, 55.9202360622414), X8 = c(67.5577910713347,
46.1891742544371, 36.4689522649804, 59.5271358261971, 49.6776114214636,
44.1995317742719, 58.4881363877987, 52.1946266979144, 62.1149998459759,
55.3748655464147), X9 = c(66.3943390258844, 45.843835703738,
37.3485122393333, 59.8591304277037, 49.387883195468, 44.4283817056918,
58.1874530826789, 53.5091378916001, 62.1187451212786, 55.3632760142297
), X10 = c(66.9748072219828, 46.20735965374, 36.7069272963502,
59.5035069226904, 48.8446530329762, 44.8753686249692, 58.0223695284058,
53.2732448917674, 61.2509571513, 54.9615424261546), age = c(55,
37, 31, 59, 49, 47, 69, 68, 69, 66)), .Names = c("X1", "X2",
"X3", "X4", "X5", "X6", "X7", "X8", "X9", "X10", "age"), row.names =
c("GSM1051533_7800246024_R03C02",
"GSM1051534_7800246024_R04C02", "GSM1051535_7800246024_R05C02",
"GSM1051536_7800246024_R06C02", "GSM1051537_7800246085_R01C01",
"GSM1051538_7800246085_R02C01", "GSM1051539_7800246085_R03C01",
"GSM1051540_7800246085_R04C01", "GSM1051541_7800246085_R05C01",
"GSM1051542_7800246085_R06C01"), class = "data.frame")
## install.packages("HH") ## if necessary
library(HH)
df.melt <- reshape2::melt(df, id.vars=c("age"))
df.melt$age.pos <- factor(df.melt$age)
position(df.melt$age.pos) <- levels(df.melt$age.pos)
## three options of x ticks and color
bwplot(value ~ age.pos, data=df.melt,
horizontal=FALSE,
panel=panel.bwplot.intermediate.hh,
scales=list(
x=list(
at=position(df.melt$age.pos), ## placement of tick labels and marks
limits=c(29, 71), ## x limits
tck=1)), ## draw tick marks
xlab="age",
main=list("value ~ age", cex=1.4))
bwplot(value ~ age.pos, data=df.melt,
horizontal=FALSE,
panel=panel.bwplot.intermediate.hh,
scales=list(
x=list(
## at=position(df.melt$age.pos), ## placement of tick labels and marks
limits=c(29, 71), ## x limits
tck=1)), ## draw tick marks
xlab="age",
main=list("value ~ age", cex=1.4))
bwplot(value ~ age.pos, data=df.melt,
horizontal=FALSE,
panel=panel.bwplot.intermediate.hh,
col="blue", ## constant color
scales=list(
x=list(
## at=position(df.melt$age.pos), ## placement of tick labels and marks
limits=c(29, 71), ## x limits
tck=1)), ## draw tick marks
xlab="age",
main=list("value ~ age", cex=1.4))
On Thu, Feb 23, 2017 at 11:52 PM, Sebastien Bihorel
<sebastien.bihorel at cognigencorp.com> wrote:
Hi, Can the boxplot design illustrated in the post (http://stackoverflow.com/questions/39849459/how-to-create-boxplots-with-a-continuous-x-axis-in-r) be reproduced with lattice or a lattice-derived function? Thank you Sebastien
______________________________________________ R-help at 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.
Thanks for your reply
----- Original Message -----
From: "Bert Gunter" <bgunter.4567 at gmail.com>
To: "Sebastien Bihorel" <sebastien.bihorel at cognigencorp.com>
Cc: "R-help" <r-help at r-project.org>
Sent: Friday, February 24, 2017 2:01:36 AM
Subject: Re: [R] Vertical boxplot with a continuous X axis
Sebastien:
The linked post is unclear: two of the rows have the same age, so
should there be 10 boxplots for the 10 rows or 9 for the 9 different
ages? I assumed the latter, as otherwise how could one disciminate
rows with the same age that have overlapping values?
For lattice, I just used age as the group= parameter to group by ages
and used panel.bwplot for the panel.groups function. My "aesthetics"
are different than shown in the linked post, but can be altered in
lattice through the panel.bwplot and par.settings parameters as
described in ?panel.bwplot:
y <- unlist(df[,-11])
age <- rep(df[,"age"],10) ## Could be done programatically
xyplot(y~age, groups = age,
panel = function(...){
panel.abline(h = seq(40,65, by=5),
v = seq(30,70, by =5),
col="lightgray")
panel.superpose(...)
},
panel.groups = function(x,y,...)
panel.bwplot(x,y,horiz=FALSE,fill = "lightgray",
pch = 16, cex=.7,col= "black",box.width = 1.5),
par.settings =list(box.rectangle = list(col="black"))
)
However, note that this too could produce a hopeless mishmosh if the
ages are close together so that the boxplots overlap; or you could end
up getting nearly invisible skinny boxes, as in the plot shown in the
linked post. So on the whole, I think you are better off treating the
ages as a factor and thereby separating them, e.g.
bwplot(y~age, fill = "lightgray", horiz = FALSE,
panel = function(...){
panel.abline(h = seq(40,65, by=5),col="lightgray")
panel.bwplot(...)
},
scales = list(x= list(lab = sort(unique(age)))),
par.settings =list(box.rectangle = list(col="black"))
)
Cheers,
Bert
Bert Gunter
"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Thu, Feb 23, 2017 at 8:52 PM, Sebastien Bihorel
<sebastien.bihorel at cognigencorp.com> wrote:
Hi, Can the boxplot design illustrated in the post (http://stackoverflow.com/questions/39849459/how-to-create-boxplots-with-a-continuous-x-axis-in-r) be reproduced with lattice or a lattice-derived function? Thank you Sebastien
______________________________________________ R-help at 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.