[R] ggplot2: connecting medians of boxes using facet_wrap. Changing median marker.
Ista Zahn
istazahn at gmail.com
Thu Sep 5 17:17:09 CEST 2013
On Thu, Sep 5, 2013 at 11:08 AM, Anna Zakrisson Braeunlich
<anna.zakrisson at su.se> wrote:
> Hi and thank you for the help and for the fast reply!
>
> A. One thing still is a problem. I have prior my first mail tried to not fill the boxes. The result is a different plot.
> If chosing to do:
>
> ggplot(mydata, aes(x = week, y = var1))
>
> instead of
>
> ggplot(mydata, aes(x = week, y = var1, fill=organism))
>
> I get the median of all the levels of organisms plotted per week and not the median per organism level per week.
> I would like to have white boxes, but to define each level of organism with a different non-filled symbol that mark the median of each box.
Ooops, sorry I missed that before. You can use
geom_boxplot(mapping=aes(group=interaction(week, organism)))
to achieve this, though it now becomes hard to tell which boxplots
correspond to which organisms.
>
> B. Can I define the shapes of the geom_point other than the default filled points that I will automatically generate when I define:
> geom_point(stat="summary", fun.y = "median", mapping=aes(shape=organism)) + # I need non-filled symbols
add
scale_shape(solid=FALSE)
or
scale_shape_manual(values = 1:3)
Best,
Ista
>
> The two versions mentioned in A are:
>
> ###################DATA########################################
> mydata<- data.frame(week = factor(rep(c("19", "21", "23", "25", "27", "29", "31", "33",
> "35", "37", "39"), each = 45*3)), #week
> station = factor(rep(c("BY31", "B1", "H2", "H3", "H4",
> "H5", "H6", "H7", "H8"), each = 15)), #station
> organism = factor(rep(c("zpl", "ses", "cy"), each = 5)), #organism
> var1 = rnorm(1485, mean = rep(c(0, 3, 15), each = 40),
> sd = rep(c(1, 3, 6), each = 20)))
>
> ###################VERSION 1####################################
> p <- ggplot(mydata, aes(x = week, y = var1)) + #here all organisms are bunted together
> geom_boxplot() +
> facet_wrap(~ station, ncol = 3) +
> theme_bw() +
> theme(strip.background = element_blank())+
> ylab("var1")+
> xlab("week") +
> geom_line(stat="summary", fun.y = "median",
> mapping=aes(linetype=organism, group=organism))+ #must add jitter if using this
> geom_point(stat="summary", fun.y = "median", mapping=aes(shape=organism)) + #must be unfilled
> theme(strip.text.x = element_text(size = 12, colour="black", family="serif", angle=00)) +
> theme(axis.text.x = element_text(size = 12, colour="black", family="serif", angle=90)) +
> theme(axis.text.y = element_text(size = 12, colour="black", family="serif", angle=00)) +
> geom_hline(yintercept=0, linetype=3) #draws dotted line at 0
>
> p
>
> ###################VERSION 2####################################
>
> p <- ggplot(mydata, aes(x = week, y = var1, fill=organism)) + #here the levels in organism are considered
> geom_boxplot() +
> facet_wrap(~ station, ncol = 3) +
> theme_bw() +
> theme(strip.background = element_blank())+
> ylab("var1")+
> xlab("week") +
> geom_line(stat="summary", fun.y = "median",
> mapping=aes(linetype=organism, group=organism))+ #must add jitter if using this
> geom_point(stat="summary", fun.y = "median", mapping=aes(shape=organism)) + #must be unfilled
> theme(strip.text.x = element_text(size = 12, colour="black", family="serif", angle=00)) +
> theme(axis.text.x = element_text(size = 12, colour="black", family="serif", angle=90)) +
> theme(axis.text.y = element_text(size = 12, colour="black", family="serif", angle=00)) +
> geom_hline(yintercept=0, linetype=3) #draws dotted line at 0
>
> p
> #############################################################################
>
>
>
>
> Anna Zakrisson Braeunlich
> PhD student
>
> Department of Ecology, Environment and Plant Sciences
> Stockholm University
> Svante Arrheniusv. 21A
> SE-106 91 Stockholm
> Sweden/Sverige
>
> Lives in Berlin.
> For paper mail:
> Katzbachstr. 21
> D-10965, Berlin - Kreuzberg
> Germany/Deutschland
>
> E-mail: anna.zakrisson at su.se
> Tel work: +49-(0)3091541281
> Mobile: +49-(0)15777374888
> LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b
>
>><((((º>`•. . • `•. .• `•. . ><((((º>`•. . • `•. .• `•. .><((((º>`•. . • `•. .• `•. .><((((º>
>
> ________________________________________
> From: Ista Zahn [istazahn at gmail.com]
> Sent: 05 September 2013 16:02
> To: Anna Zakrisson Braeunlich
> Cc: r-help at r-project.org
> Subject: Re: [R] ggplot2: connecting medians of boxes using facet_wrap. Changing median marker.
>
> Hi Anna,
>
> On Thu, Sep 5, 2013 at 6:13 AM, Anna Zakrisson Braeunlich
> <anna.zakrisson at su.se> wrote:
>> # Dear all,
>>
>> # Thank you for taking your time.
>>
>> # What I would like to do:
>>
>> # (Run the code below to see what I am referring to)
>>
>> # I want lines connecting the medians of of the boxes. I do not want a function, just a simple,
>> # straight connection between points. I also would like the lines to be different: lty=c(1:3)
>
> geom_line(stat="summary", fun.y = "median",
> mapping=aes(linetype=organism, group=organism))
>
>>
>> # Furthermore, I wish to change the line/dot marking the medians to be pch=c(1:3). It seems not to be so simple when using facet_wrap? I have obviously missed something obvious.
>
> geom_point(stat="summary", fun.y = "median", mapping=aes(shape=organism)) +
>
>>
>> # Finally, I would like the boxes to be filled white and to have the legend reflecting this.
>
> Then don't tell ggplot to color them. Change
>
> ggplot(mydata, aes(x = week, y = var1, fill = organism))
>
> to
>
> ggplot(mydata, aes(x = week, y = var1))
>>
>> # I know that this was many questions, I apologize if some may seem basic. It is just that I am
>> # "jumping packages" the whole time and sometimes par() adjustments work and sometimes not.
>> # I have searched alot for answers, but as a ggplot2 beginner, I have failed to find a solution
>> # to my problems above.
>
>
> Hope this helps!
>
> Best,
> Ista
>
>>
>> # I would like to thank the programmers for a great package. The layer principle is much easier to work with.
>>
>> ####
>>
>> # Some dummy data:
>> mydata<- data.frame(week = factor(rep(c("19", "21", "23", "25", "27", "29", "31", "33",
>> "35", "37", "39"), each = 45*3)), #week
>> station = factor(rep(c("BY31", "B1", "H2", "H3", "H4",
>> "H5", "H6", "H7", "H8"), each = 15)), #station
>> organism = factor(rep(c("zpl", "ses", "cy"), each = 5)), #organism
>> var1 = rnorm(1485, mean = rep(c(0, 3, 15), each = 40),
>> sd = rep(c(1, 3, 6), each = 20)))
>>
>> p <- ggplot(mydata, aes(x = week, y = var1, fill = organism)) +
>> geom_boxplot() +
>> facet_wrap(~ station, ncol = 3) +
>> theme_bw() +
>> theme(strip.background = element_blank())+
>> ylab("var1")+
>> xlab("week") +
>> geom_smooth(aes(group = 1), method="lm", se = F) + #Here is my problem.
>> theme(strip.text.x = element_text(size = 12, colour="black", family="serif", angle=00)) +
>> theme(axis.text.x = element_text(size = 12, colour="black", family="serif", angle=90)) +
>> theme(axis.text.y = element_text(size = 12, colour="black", family="serif", angle=00)) +
>> geom_hline(yintercept=0, linetype=3) #draws dotted line at 0
>>
>> p
>>
>> # method="lm" is definately wrong,
>> # I just added it to be a ble to draw some lines at all.
>> # I also suspect geom_smooth to be wrong.
>> ### TO CLARIFY: I want the medians connected within each level. cy medians connected and
>> # and ses medians connected and zpl connected. Not cy-ses-zpl, but that is perhaps obvious.
>> ### Thank you for your time!
>> # with kind regards
>> # A. Zakrisson
>>
>>
>>
>> Anna Zakrisson Braeunlich
>> PhD student
>>
>> Department of Ecology, Environment and Plant Sciences
>> Stockholm University
>> Svante Arrheniusv. 21A
>> SE-106 91 Stockholm
>> Sweden/Sverige
>>
>> Lives in Berlin.
>> For paper mail:
>> Katzbachstr. 21
>> D-10965, Berlin - Kreuzberg
>> Germany/Deutschland
>>
>> E-mail: anna.zakrisson at su.se
>> Tel work: +49-(0)3091541281
>> Mobile: +49-(0)15777374888
>> LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b
>>
>>><((((º>`•. . • `•. .• `•. . ><((((º>`•. . • `•. .• `•. .><((((º>`•. . • `•. .• `•. .><((((º>
>>
>> [[alternative HTML version deleted]]
>>
>>
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