[R] annotation help in ggplot2
Moshiur Rahman
mr@hm@nku|mrt @end|ng |rom gm@||@com
Sat Sep 21 00:20:12 CEST 2019
Thanks everyone especially Rishi to solve
this issue
Regards,
Moshichi
On Fri, Sep 20, 2019 at 22:26 Jeff Newmiller <jdnewmil using dcn.davis.ca.us>
wrote:
> Using this list as a labor pool to procure code for generating
> publication-quality plots is abuse. Please read the Posting Guide and the
> documentation for the ggplot package or go pay someone offlist for their
> services.
>
> On September 20, 2019 4:15:18 AM PDT, Moshiur Rahman <
> mrahmankufmrt using gmail.com> wrote:
> >Thanks a lot Rishi for your very cordial effort and great help. But
> >still I
> >need some help to improve it as the plot doesn't clearly depict which
> >female belongs to which family and this can be detected by drawing a
> >line
> >from 1-4 for F1, 5-8 for F2....
> >
> >Another problem I can see that the position of MID (P1,2,3...) is not
> >looking well which are somehow noisy.
> >
> >Finally, can we drop the bars at the bottom of x-axis that I did
> >with scale_y_continuous?
> >
> >Please do me some favour to complete this plot which I need for a
> >publication.
> >
> >With kind regards,
> >
> >Moshi
> >
> >On Fri, Sep 20, 2019 at 7:45 PM ঋষি ( ऋषि / rIsHi )
> ><rishi.dasroy using gmail.com>
> >wrote:
> >
> >> Here is the solution inspired by this post
> >>
> >
> https://stackoverflow.com/questions/18165863/multirow-axis-labels-with-nested-grouping-variables
> >>
> >>
> >> > data$Female <- factor(data$Female, levels =
> >> c("F1","F2","F3","F4","F5","F6","F7","F8","F9","F10"))
> >> >
> >>
>
> >ggplot(data,aes(x=family,y=offs.surv.perct,fill=treat))+geom_bar(stat="identity",
> >> position="dodge")+
> >> geom_text(aes(label = MID), angle=90)+
> >> facet_wrap(~Female, strip.position = "bottom", scales =
> >"free_x",nrow=1)+
> >> theme(panel.spacing = unit(0, "lines"),
> >> strip.background = element_blank(),
> >> strip.placement = "outside")
> >>
> >>
> >> On Fri, Sep 20, 2019 at 11:51 AM Moshiur Rahman
> ><mrahmankufmrt using gmail.com>
> >> wrote:
> >>
> >>> Thanks Rishi,
> >>>
> >>> Please find attached the data herewith.
> >>>
> >>>
> >>>
> >>> On Fri, Sep 20, 2019 at 5:48 PM ঋষি ( ऋषि / rIsHi ) <
> >>> rishi.dasroy using gmail.com> wrote:
> >>>
> >>>> There are no attached data .
> >>>>
> >>>> On Fri, Sep 20, 2019 at 11:40 AM Moshiur Rahman
> ><mrahmankufmrt using gmail.com>
> >>>> wrote:
> >>>>
> >>>>> Dear ggplot2 experts,
> >>>>>
> >>>>> I'm struggling to make a plot having family id in x-axis and
> >female id
> >>>>> below that family id where each 4 families have a single female
> >id.
> >>>>>
> >>>>> I also need to add male id on top of each bar which I can do
> >before
> >>>>> grid.arrange, but fail after doing it. So, any suggestions?
> >>>>>
> >>>>> Please find below my codes and help me to complete it perfectly.
> >>>>> #data
> >>>>> data <- read.table("R-help_ggplot2.csv", header=TRUE, sep=",")
> >>>>> names(data)
> >>>>> #packages
> >>>>> library(ggplot2)
> >>>>> library(grid)
> >>>>> library(gridExtra)
> >>>>> library(scales)
> >>>>> library(ggpubr)
> >>>>> #plot codes
> >>>>> p1 =
> >>>>>
> >ggplot(data,aes(x=factor(family),y=offs.surv.perct,fill=factor(treat)))+
> >>>>> geom_bar(stat="identity", position="dodge")+
> >>>>> #facet_wrap(~ Female)+
> >>>>> geom_bar(stat="identity", position="dodge", colour="black",
> >>>>> show.legend= TRUE) + # show_guide = TRUE gives legend boarder
> >>>>> #geom_hline(yintercept=15, size=0.5, linetype = 2)+ ### middle
> >line
> >>>>> scale_fill_manual(values=c("grey", "white")) + # grey80 is
> >closer to
> >>>>> white than black
> >>>>> xlab("Family") +
> >>>>> ylab (expression(paste("Offspring survival rate (%)"))) +
> >>>>> #coord_cartesian(xlim=c(0,40), ylim=c(0,60), clip="off")+
> >>>>> scale_y_continuous(expand = c(0, 0), limits = c(0, 60))+
> >>>>> theme(legend.title = element_text(colour="black", size=12))+
> >>>>> theme(legend.text = element_text(colour="black", size=11))+
> >>>>> theme(legend.background = element_blank())+
> >>>>> theme(legend.key = element_blank())+
> >>>>> theme(legend.box.background = element_blank())+
> >>>>> theme(legend.key.size = unit(2, "mm"),legend.key.width =
> >>>>> unit(0.5,"cm"))+
> >>>>> theme(legend.position=c(0.05,0.9),legend.direction
> >>>>> ="vertical",legend.box = "vertical")+ # add legend on top
> >>>>> theme(panel.background = element_rect(fill = "transparent"))+
> >>>>> theme(axis.line = element_line(colour =
> >>>>> "black"),axis.text.x=element_text(size=10,
> >>>>> colour="black"),axis.text.y=element_text(size=10, colour="black"),
> >>>>> axis.title.y = element_text(size=12, colour =
> >>>>> "black",margin=margin(0,5,0,0)),
> >>>>> axis.title.x = element_blank(),
> >>>>> strip.text.x = element_blank(),# remove top level title
> >(high
> >>>>> and
> >>>>> low)
> >>>>> strip.background = element_blank(),# remove top level
> >background
> >>>>> panel.grid.major = element_blank(),# remove grid line
> >within the
> >>>>> plot
> >>>>> panel.grid.minor = element_blank(),
> >>>>> panel.border = element_blank())
> >>>>> p1
> >>>>>
> >>>>> ### legend correction
> >>>>> p2<- p1 + guides(fill = guide_legend(title="Fertilization
> >>>>> group",keywidth =
> >>>>> 1,keyheight = 1,
> >>>>> title.theme = element_text(size=12,
> >colour
> >>>>> =
> >>>>> "black", angle = 0)))+
> >>>>> theme(legend.text = element_text(size = 12, colour = "black",
> >angle =
> >>>>> 0))
> >>>>>
> >>>>> p2
> >>>>>
> >>>>> ###plot margins
> >>>>> p3<-p2+theme(plot.margin = unit(c(1,1,1.7,1), "lines"))
> >>>>> p3
> >>>>>
> >>>>> #x-axis label
> >>>>> p4<-grid.arrange(
> >>>>> p3,
> >>>>> bottom = textGrob(
> >>>>> "Family and female number",
> >>>>> gp = gpar(fontsize = 12, cex=1), #fontface = "bold",
> >>>>> vjust = 0.5, hjust = 0.5,x = 0.52))
> >>>>>
> >>>>> # annotation (NOT WORKING)
> >>>>> p5<-p4+annotate("text", label = "M1", x = 1, y = 25.03, fontface =
> >1,
> >>>>> size=3,angle = 90)
> >>>>> p5
> >>>>> p6<-p5+annotate("text", label = "M2", x = 2, y = 18.37, fontface =
> >1,
> >>>>> size=3,angle = 90)
> >>>>> p6
> >>>>> p7<-p6+annotate("text", label = "M3", x = 3, y = 21.7, fontface =
> >1,
> >>>>> size=3,angle = 90)
> >>>>> p7
> >>>>> p8<-p7+annotate("text", label = "M1-2-3", x = 4, y = 19.1,
> >fontface= 1,
> >>>>> size=3,angle = 90)
> >>>>> p8
> >>>>> Fig1.1<-p8+annotate("segment", size=0.3, x=c(1,1,4),xend=c(1,4,4),
> >>>>> y= c(26,28,28), yend=c(28,28,21))+
> >>>>> annotate("text",x=2.45,y=29.5,fontface = 1, size=3,angle =
> >>>>> 90,label=c("F1"))
> >>>>>
> >>>>> Fig1.1
> >>>>>
> >>>>> Please find attached also my data.
> >>>>>
> >>>>> Any assistance will be highly appreciated.
> >>>>>
> >>>>> Regards,
> >>>>>
> >>>>> Moshi
> >>>>>
> >>>>>
> >>>>> JSPS Postdoctoral Fellow
> >>>>> Laboratory of Population Biology
> >>>>> Department of Marine Biosciences
> >>>>> Graduate School of Marine Science and Technology
> >>>>> Tokyo University of Marine Science and Technology
> >>>>> 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
> >>>>> Mobile: 050-6874-9072
> >>>>> ______________________________________________
> >>>>> R-help using 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.
> >>>>>
> >>>>
> >>>>
> >>>> --
> >>>>
> >>>>
> >>>>
> >>>> With regards
> >>>> Rishi Das Roy
> >>>>
> >>>
> >>>
> >>> --
> >>> Md. Moshiur Rahman, PhD
> >>>
> >>> JSPS Postdoctoral Fellow
> >>> Laboratory of Population Biology
> >>> Department of Marine Biosciences
> >>> Graduate School of Marine Science and Technology
> >>> Tokyo University of Marine Science and Technology
> >>> 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
> >>> Mobile: 050-6874-9072
> >>>
> >>> .........................
> >>>
> >>> Professor
> >>> Fisheries and Marine Resource Technology Discipline
> >>> Khulna University, Khulna - 9208
> >>> BANGLADESH.
> >>> Google scholar:
> >>> https://scholar.google.com.au/citations?user=uElrJSsAAAAJ&hl=en
> >>> ResearchGate:
> >https://www.researchgate.net/profile/Md_Moshiur_Rahman2
> >>> ORCID: https://orcid.org/my-orcid
> >>>
> >>
> >>
> >> --
> >>
> >>
> >>
> >> With regards
> >> Rishi Das Roy
> >>
>
> --
> Sent from my phone. Please excuse my brevity.
>
--
Md. Moshiur Rahman, PhD
JSPS Postdoctoral Fellow
Laboratory of Population Biology
Department of Marine Biosciences
Graduate School of Marine Science and Technology
Tokyo University of Marine Science and Technology
4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
Mobile: 050-6874-9072
.........................
Professor
Fisheries and Marine Resource Technology Discipline
Khulna University, Khulna - 9208
BANGLADESH.
Google scholar:
https://scholar.google.com.au/citations?user=uElrJSsAAAAJ&hl=en
ResearchGate: https://www.researchgate.net/profile/Md_Moshiur_Rahman2
ORCID: https://orcid.org/my-orcid
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