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PIKAL Petr

2015-Feb-06 11:09 UTC

[R] suggestion for optimal plotting to show significant differences

Dear all

I would like to ask for your opinion about possible graphical representation of
such data.
> dput(test)structure(list(item = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("A",
"B"), class = "factor"), day = c(0L, 100L, 200L, 300L, 400L,
500L, 0L, 100L, 200L, 300L, 400L, 500L, 0L, 100L, 200L, 300L,
400L, 500L, 0L, 100L, 200L, 300L, 400L, 500L, 0L, 100L, 200L,
300L, 400L, 500L, 0L, 100L, 200L, 300L, 400L, 500L), set = c(1L,
1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L,
3L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L,
3L, 3L, 3L), value = c(1.08163365169503, 2.61998412608805, 3.07820466606394,
4.44993419381934, 5.29163171545805, 6.29155990999293, -0.123163011367676,
2.07767236834003, 2.32537052874901, 3.09372794501084, 6.65273721166635,
5.92304962329131, 1.50504697705548, 2.66253728086866, 2.63420157418685,
2.78195098580416, 6.47578642973288, 5.89587443775143, 0.848864231485078,
1.27549677119713, 2.19573089053609, 2.45659926134292, 5.15424403414103,
5.4813151140983, 1.25731482647214, 2.09662105167973, 1.75954023316977,
4.81624002288939, 4.65029189325307, 6.39946904227214, 0.944996929887344,
1.74667265331284, 2.42956264345558, 5.17852980415141, 3.5453435965834,
6.9011238437191)), .Names = c("item", "day",
"set", "value"), row.names = c(NA,
-36L), class = "data.frame")>
One option I came with is

library(ggplot2)
p<-ggplot(test, aes(x=day, y=value, colour=item))
p+geom_point()+stat_smooth(method="lm", formula= y~poly(x,2))

but -
I have more items (around 5-10), and I want to show if the difference between
items is or is not significant. The actual development of value with day is
usually not linear nor growing steadily and actually I cannot usually evaluate
some analytical equation for my data to compare equation parameters.

I thought about boxplots, but there is not many repetitions and actually 5+
boxplots can be quite messy.

I can plot only mean for each set and item but in that case I lose information
if the difference is or is not significant.

I appreciate any suggestion.

Best regards
Petr








________________________________
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Richard M. Heiberger

2015-Feb-06 17:14 UTC

head link

[R] suggestion for optimal plotting to show significant differences

I would try one of these illustrations for starts.
interaction2wt (two-way tables) is designed to be used with aov() for testing.
interaction2wt shows all main effects and all two-way interactions for
many factors.



test <-
structure(list(item = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("A",
"B"), class = "factor"), day = c(0L, 100L, 200L, 300L, 400L,
500L, 0L, 100L, 200L, 300L, 400L, 500L, 0L, 100L, 200L, 300L,
400L, 500L, 0L, 100L, 200L, 300L, 400L, 500L, 0L, 100L, 200L,
300L, 400L, 500L, 0L, 100L, 200L, 300L, 400L, 500L), set = c(1L,
1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L,
3L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L,
3L, 3L, 3L), value = c(1.08163365169503, 2.61998412608805, 3.07820466606394,
4.44993419381934, 5.29163171545805, 6.29155990999293, -0.123163011367676,
2.07767236834003, 2.32537052874901, 3.09372794501084, 6.65273721166635,
5.92304962329131, 1.50504697705548, 2.66253728086866, 2.63420157418685,
2.78195098580416, 6.47578642973288, 5.89587443775143, 0.848864231485078,
1.27549677119713, 2.19573089053609, 2.45659926134292, 5.15424403414103,
5.4813151140983, 1.25731482647214, 2.09662105167973, 1.75954023316977,
4.81624002288939, 4.65029189325307, 6.39946904227214, 0.944996929887344,
1.74667265331284, 2.42956264345558, 5.17852980415141, 3.5453435965834,
6.9011238437191)), .Names = c("item", "day",
"set", "value"), row.names = c(NA,
-36L), class = "data.frame")



library(HH)

test$set <- factor(test$set)
test$day <- factor(test$day)
test$item <- factor(test$item)

interaction2wt(value ~ item * day * set, data=test)

test$item.day <- interaction(test$item, test$day)
position(test$item.day) <- outer(c(-10,10), as.numeric(levels(test$day)),
`+`)

xyplot(value ~ as.position(item.day) | set, groups=item,
        data=test, horizontal=FALSE, pch=c(17,16),
        xlab="day",
        scales=list(
          x=list(
            alternating=1,
            at=levels(test$day), ## placement of tick labels and marks
            tck=1)),
        key=list(
          text=list(c("A","B"),
col=c("blue","red")),
          points=list(pch=c(17, 16), col=c("blue","red")),
       space="top", columns=2, border=TRUE),
       layout=c(3,1))


## see also the examples in
demo(package="HH", bwplot.examples)

On Fri, Feb 6, 2015 at 6:09 AM, PIKAL Petr <petr.pikal at precheza.cz>
wrote:> Dear all
>
> I would like to ask for your opinion about possible graphical
representation of such data.
>
>> dput(test)
> structure(list(item = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L,
> 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label =
c("A",
> "B"), class = "factor"), day = c(0L, 100L, 200L, 300L,
400L,
> 500L, 0L, 100L, 200L, 300L, 400L, 500L, 0L, 100L, 200L, 300L,
> 400L, 500L, 0L, 100L, 200L, 300L, 400L, 500L, 0L, 100L, 200L,
> 300L, 400L, 500L, 0L, 100L, 200L, 300L, 400L, 500L), set = c(1L,
> 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L,
> 3L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L,
> 3L, 3L, 3L), value = c(1.08163365169503, 2.61998412608805,
3.07820466606394,
> 4.44993419381934, 5.29163171545805, 6.29155990999293, -0.123163011367676,
> 2.07767236834003, 2.32537052874901, 3.09372794501084, 6.65273721166635,
> 5.92304962329131, 1.50504697705548, 2.66253728086866, 2.63420157418685,
> 2.78195098580416, 6.47578642973288, 5.89587443775143, 0.848864231485078,
> 1.27549677119713, 2.19573089053609, 2.45659926134292, 5.15424403414103,
> 5.4813151140983, 1.25731482647214, 2.09662105167973, 1.75954023316977,
> 4.81624002288939, 4.65029189325307, 6.39946904227214, 0.944996929887344,
> 1.74667265331284, 2.42956264345558, 5.17852980415141, 3.5453435965834,
> 6.9011238437191)), .Names = c("item", "day",
"set", "value"), row.names = c(NA,
> -36L), class = "data.frame")
>>
>
> One option I came with is
>
> library(ggplot2)
> p<-ggplot(test, aes(x=day, y=value, colour=item))
> p+geom_point()+stat_smooth(method="lm", formula= y~poly(x,2))
>
> but -
> I have more items (around 5-10), and I want to show if the difference
between items is or is not significant. The actual development of value with day
is usually not linear nor growing steadily and actually I cannot usually
evaluate some analytical equation for my data to compare equation parameters.
>
> I thought about boxplots, but there is not many repetitions and actually 5+
boxplots can be quite messy.
>
> I can plot only mean for each set and item but in that case I lose
information if the difference is or is not significant.
>
> I appreciate any suggestion.
>
> Best regards
> Petr
>
>
>
>
>
>
>
>
> ________________________________
> Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou
ur?eny pouze jeho adres?t?m.
> Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen?
jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze
sv?ho syst?mu.
> Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email
jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat.
> Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi
?i zpo?d?n?m p?enosu e-mailu.
>
> V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?:
> - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en?
smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu.
> - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout;
Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany p??jemce
s dodatkem ?i odchylkou.
> - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve v?slovn?m
dosa?en?m shody na v?ech jej?ch n?le?itostech.
> - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za
spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n nebo
p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto emailu
p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich existence je
adres?tovi ?i osob? j?m zastoupen? zn?m?.
>
> This e-mail and any documents attached to it may be confidential and are
intended only for its intended recipients.
> If you received this e-mail by mistake, please immediately inform its
sender. Delete the contents of this e-mail with all attachments and its copies
from your system.
> If you are not the intended recipient of this e-mail, you are not
authorized to use, disseminate, copy or disclose this e-mail in any manner.
> The sender of this e-mail shall not be liable for any possible damage
caused by modifications of the e-mail or by delay with transfer of the email.
>
> In case that this e-mail forms part of business dealings:
> - the sender reserves the right to end negotiations about entering into a
contract in any time, for any reason, and without stating any reasoning.
> - if the e-mail contains an offer, the recipient is entitled to immediately
accept such offer; The sender of this e-mail (offer) excludes any acceptance of
the offer on the part of the recipient containing any amendment or variation.
> - the sender insists on that the respective contract is concluded only upon
an express mutual agreement on all its aspects.
> - the sender of this e-mail informs that he/she is not authorized to enter
into any contracts on behalf of the company except for cases in which he/she is
expressly authorized to do so in writing, and such authorization or power of
attorney is submitted to the recipient or the person represented by the
recipient, or the existence of such authorization is known to the recipient of
the person represented by the recipient.
> ______________________________________________
> 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
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PIKAL Petr

2015-Feb-09 11:01 UTC

head link

[R] suggestion for optimal plotting to show significant differences

Hallo Richard.

I tried your suggestion but it seems to be no better than simple ggplot. Let me
extend the example a bit to 8 items which is more realistic.

item<-rep(letters[1:8], each=18)
day<-rep((0:5)*100, 24)
set<-rep(rep(1:3, each=6), 8)
test<-data.frame(item, day, set)
set.seed(111)
test$value<-(test$day/100+1)+rnorm(144)
test$value<-test$value+(as.numeric(test$item)*1.3)

Value is increasing during time (day) for each tested subject (item), each item
is measured 3 times (set) each day.

Here is some graph
p<-ggplot(test, aes(x=day, y=value, colour=item))
p+geom_point()+stat_smooth(method="lm", formula= y~poly(x,2))

I can do lm or aov, however I am not sure about proper formula.

fit<-lm(value~day, data=test)
summary(fit)
# this shows that value is increasing with day

fit<-lm(value~day/item, data=test)
summary(fit)
# this suggests that value is decreasing with day (which is wrong)

fit<-lm(value~day*item, data=test)
summary(fit)
# and this tells me that value is increasing with day and items have different
intercepts but the same rate of growth (I hope I got it right).

I do not have your book available but I went through help pages.

Your interaction graph is not much better than ggplot.
I can do

interaction2wt(value ~ item * day, data=test)

which probably is closer to actual problem.

The basic problem is that increase of value with days is in fact not linear and
actually it can increase in the beginning and then stagnate or it can stagnate
in beginning and then increase. I am not aware of any way how to compare time
behaviour of different items in such situations if I cannot state some common
formula in which case I would use probably nlme.

Thank for your insight, I try to go through it more deeply.

Best regards
Petr

> -----Original Message-----
> From: Richard M. Heiberger [mailto:rmh at temple.edu]
> Sent: Friday, February 06, 2015 6:14 PM
> To: PIKAL Petr
> Cc: r-help at r-project.org
> Subject: Re: [R] suggestion for optimal plotting to show significant
> differences
>
> I would try one of these illustrations for starts.
> interaction2wt (two-way tables) is designed to be used with aov() for
> testing.
> interaction2wt shows all main effects and all two-way interactions for
> many factors.
>
>
>
> test <-
> structure(list(item = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
> 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("A",
"B"), class > "factor"), day = c(0L, 100L, 200L, 300L,
400L, 500L, 0L, 100L, 200L,
> 300L, 400L, 500L, 0L, 100L, 200L, 300L, 400L, 500L, 0L, 100L, 200L,
> 300L, 400L, 500L, 0L, 100L, 200L, 300L, 400L, 500L, 0L, 100L, 200L,
> 300L, 400L, 500L), set = c(1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L,
> 2L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L,
> 2L, 3L, 3L, 3L, 3L, 3L, 3L), value = c(1.08163365169503,
> 2.61998412608805, 3.07820466606394, 4.44993419381934, 5.29163171545805,
> 6.29155990999293, -0.123163011367676, 2.07767236834003,
> 2.32537052874901, 3.09372794501084, 6.65273721166635, 5.92304962329131,
> 1.50504697705548, 2.66253728086866, 2.63420157418685, 2.78195098580416,
> 6.47578642973288, 5.89587443775143, 0.848864231485078,
> 1.27549677119713, 2.19573089053609, 2.45659926134292, 5.15424403414103,
> 5.4813151140983, 1.25731482647214, 2.09662105167973, 1.75954023316977,
> 4.81624002288939, 4.65029189325307, 6.39946904227214,
> 0.944996929887344, 1.74667265331284, 2.42956264345558,
> 5.17852980415141, 3.5453435965834, 6.9011238437191)), .Names >
c("item", "day", "set", "value"),
row.names = c(NA, -36L), class > "data.frame")
>
>
>
> library(HH)
>
> test$set <- factor(test$set)
> test$day <- factor(test$day)
> test$item <- factor(test$item)
>
> interaction2wt(value ~ item * day * set, data=test)
>
> test$item.day <- interaction(test$item, test$day)
> position(test$item.day) <- outer(c(-10,10),
> as.numeric(levels(test$day)), `+`)
>
> xyplot(value ~ as.position(item.day) | set, groups=item,
>         data=test, horizontal=FALSE, pch=c(17,16),
>         xlab="day",
>         scales=list(
>           x=list(
>             alternating=1,
>             at=levels(test$day), ## placement of tick labels and marks
>             tck=1)),
>         key=list(
>           text=list(c("A","B"),
col=c("blue","red")),
>           points=list(pch=c(17, 16),
col=c("blue","red")),
>        space="top", columns=2, border=TRUE),
>        layout=c(3,1))
>
>
> ## see also the examples in
> demo(package="HH", bwplot.examples)
>
> On Fri, Feb 6, 2015 at 6:09 AM, PIKAL Petr <petr.pikal at
precheza.cz>
> wrote:
> > Dear all
> >
> > I would like to ask for your opinion about possible graphical
> representation of such data.
> >
> >> dput(test)
> > structure(list(item = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
> > 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
> > 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("A",
"B"), class
> > > "factor"), day = c(0L, 100L, 200L, 300L, 400L, 500L,
0L, 100L, 200L,
> > 300L, 400L, 500L, 0L, 100L, 200L, 300L, 400L, 500L, 0L, 100L, 200L,
> > 300L, 400L, 500L, 0L, 100L, 200L, 300L, 400L, 500L, 0L, 100L, 200L,
> > 300L, 400L, 500L), set = c(1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L,
> 2L,
> > 2L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L,
> > 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L), value = c(1.08163365169503,
> > 2.61998412608805, 3.07820466606394, 4.44993419381934,
> > 5.29163171545805, 6.29155990999293, -0.123163011367676,
> > 2.07767236834003, 2.32537052874901, 3.09372794501084,
> > 6.65273721166635, 5.92304962329131, 1.50504697705548,
> > 2.66253728086866, 2.63420157418685, 2.78195098580416,
> > 6.47578642973288, 5.89587443775143, 0.848864231485078,
> > 1.27549677119713, 2.19573089053609, 2.45659926134292,
> > 5.15424403414103, 5.4813151140983, 1.25731482647214,
> 2.09662105167973,
> > 1.75954023316977, 4.81624002288939, 4.65029189325307,
> > 6.39946904227214, 0.944996929887344, 1.74667265331284,
> > 2.42956264345558, 5.17852980415141, 3.5453435965834,
> > 6.9011238437191)), .Names = c("item", "day",
"set", "value"),
> > row.names = c(NA, -36L), class = "data.frame")
> >>
> >
> > One option I came with is
> >
> > library(ggplot2)
> > p<-ggplot(test, aes(x=day, y=value, colour=item))
> > p+geom_point()+stat_smooth(method="lm", formula=
y~poly(x,2))
> >
> > but -
> > I have more items (around 5-10), and I want to show if the difference
> between items is or is not significant. The actual development of value
> with day is usually not linear nor growing steadily and actually I
> cannot usually evaluate some analytical equation for my data to compare
> equation parameters.
> >
> > I thought about boxplots, but there is not many repetitions and
> actually 5+ boxplots can be quite messy.
> >
> > I can plot only mean for each set and item but in that case I lose
> information if the difference is or is not significant.
> >
> > I appreciate any suggestion.
> >
> > Best regards
> > Petr
> >
> >
> >
> >
> >
> >
> >
> >
> > ________________________________
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________________________________
Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny
pouze jeho adres?t?m.
Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho
odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho
syst?mu.
Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email
jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat.
Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i
zpo?d?n?m p?enosu e-mailu.

V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?:
- vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? smlouvy, a
to z jak?hokoliv d?vodu i bez uveden? d?vodu.
- a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout;
Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany p??jemce
s dodatkem ?i odchylkou.
- trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve v?slovn?m
dosa?en?m shody na v?ech jej?ch n?le?itostech.
- odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za spole?nost
??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n nebo p?semn?
pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto emailu p??padn?
osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich existence je adres?tovi
?i osob? j?m zastoupen? zn?m?.

This e-mail and any documents attached to it may be confidential and are
intended only for its intended recipients.
If you received this e-mail by mistake, please immediately inform its sender.
Delete the contents of this e-mail with all attachments and its copies from your
system.
If you are not the intended recipient of this e-mail, you are not authorized to
use, disseminate, copy or disclose this e-mail in any manner.
The sender of this e-mail shall not be liable for any possible damage caused by
modifications of the e-mail or by delay with transfer of the email.

In case that this e-mail forms part of business dealings:
- the sender reserves the right to end negotiations about entering into a
contract in any time, for any reason, and without stating any reasoning.
- if the e-mail contains an offer, the recipient is entitled to immediately
accept such offer; The sender of this e-mail (offer) excludes any acceptance of
the offer on the part of the recipient containing any amendment or variation.
- the sender insists on that the respective contract is concluded only upon an
express mutual agreement on all its aspects.
- the sender of this e-mail informs that he/she is not authorized to enter into
any contracts on behalf of the company except for cases in which he/she is
expressly authorized to do so in writing, and such authorization or power of
attorney is submitted to the recipient or the person represented by the
recipient, or the existence of such authorization is known to the recipient of
the person represented by the recipient.

R help - Feb 2015 - suggestion for optimal plotting to show significant differences

[R] suggestion for optimal plotting to show significant differences

[R] suggestion for optimal plotting to show significant differences

[R] suggestion for optimal plotting to show significant differences