Hi,
I created a bar plot with this code:
library(ggplot2)
df <- data.frame("prop" = c(7.75,70.42), "Name" =
c("All Genes","RG Genes"))
p<-ggplot(data=df, aes(x=Name, y=prop,fill=Name)) +
geom_bar(stat="identity")+ labs(x="", y = "Proportion
of cis
EQTLs")+ scale_fill_brewer(palette="Greens") +
theme_minimal()+theme(legend.position = "none")
p
What do I need to change in my plot so that I have plot with p value
shown on the attached figure?
Thanks
Ana
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You will need to add stat_compare_means. Take a look at here. http://www.sthda.com/english/articles/24-ggpubr-publication-ready-plots/76-add-p-values-and-significance-levels-to-ggplots/ library(ggpubr) p + stat_compare_means() Should be fine. Vivek On Fri, Sep 27, 2019 at 7:29 PM Ana Marija <sokovic.anamarija at gmail.com> wrote:> Hi, > > I created a bar plot with this code: > > library(ggplot2) > df <- data.frame("prop" = c(7.75,70.42), "Name" = c("All Genes","RG > Genes")) > p<-ggplot(data=df, aes(x=Name, y=prop,fill=Name)) + > geom_bar(stat="identity")+ labs(x="", y = "Proportion of cis > EQTLs")+ scale_fill_brewer(palette="Greens") + > theme_minimal()+theme(legend.position = "none") > p > > What do I need to change in my plot so that I have plot with p value > shown on the attached figure? > > Thanks > Ana > ______________________________________________ > 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. >-- ---------------------------------------------------------- Vivek Das, PhD [[alternative HTML version deleted]]
Ah, this is a single observation and not pvalue calculation over a distribution. You don?t seem to have a spread. Here your code seemed like it was over all genes(more than 1) vs RG genes(also more than one). But it is basically an observation of difference of 2 values. So it doesn?t need to calculate any pvalues. Probability calculation is only needed when you have distribution of data in each arm to make Ho(null hypothesis) thar ststes condition 1 vs condition 2 have no difference but when you compute the distribution, you find a difference that rejects your Null and makes the alternative hypotheses true. Just observed your ?prop? is between only two values. So no reason for comparing since there is no distribution. Just make barplot and compute the Delta that can be difference between 70.42-7.75 or fold change 70.42/7.75. If they are absolute value you can also scale them in log scale and do the same. Hope this helps. Good luck. Vivek On Fri, Sep 27, 2019 at 9:32 PM Ana Marija <sokovic.anamarija at gmail.com> wrote:> Hi Vivek, > > Thanks for getting back to me and yes that is what I tried: > > library(ggpubr) > library(ggplot2) > df <- data.frame("prop" = c(7.75,70.42), "Name" = c("All Genes","RG > Genes")) > my_comparisons <- list(c("All Genes","RG Genes")) > > p <-ggbarplot(df, x="Name", y="prop",fill="Name",legend ="",color > "white",palette = "jco",xlab = FALSE,ylab="cis eqtl per gene") > > p + stat_compare_means(comparisons=my_comparisons) > > I got p value 1, I am wondering does putting here p value makes sense > because I don't have any distribution, I just have these two numbers > on y axis: > "prop" = c(7.75,70.42) > > Please advise, > > Thanks > Ana > > > On Fri, Sep 27, 2019 at 11:21 PM Vivek Das <vd4mmind at gmail.com> wrote: > > > > You will need to add stat_compare_means. Take a look at here. > > > > > > > http://www.sthda.com/english/articles/24-ggpubr-publication-ready-plots/76-add-p-values-and-significance-levels-to-ggplots/ > > > > library(ggpubr) > > p + stat_compare_means() > > > > Should be fine. > > > > Vivek > > > > On Fri, Sep 27, 2019 at 7:29 PM Ana Marija <sokovic.anamarija at gmail.com> > wrote: > >> > >> Hi, > >> > >> I created a bar plot with this code: > >> > >> library(ggplot2) > >> df <- data.frame("prop" = c(7.75,70.42), "Name" = c("All Genes","RG > Genes")) > >> p<-ggplot(data=df, aes(x=Name, y=prop,fill=Name)) + > >> geom_bar(stat="identity")+ labs(x="", y = "Proportion of cis > >> EQTLs")+ scale_fill_brewer(palette="Greens") + > >> theme_minimal()+theme(legend.position = "none") > >> p > >> > >> What do I need to change in my plot so that I have plot with p value > >> shown on the attached figure? > >> > >> Thanks > >> Ana > >> ______________________________________________ > >> 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. > > > > -- > > ---------------------------------------------------------- > > > > Vivek Das, PhD >-- ---------------------------------------------------------- Vivek Das, PhD [[alternative HTML version deleted]]
Awesome, thanks! Yes those two numbers on y axis I calculated as (#of EQTLs)/(#of genes) and the same for the other, RG condition. So implicitly I do have a spread just that data was not used to plot this, only those ratios. Is in this case still p value not necessary? On Fri, 27 Sep 2019 at 23:43, Vivek Das <vd4mmind at gmail.com> wrote:> Ah, this is a single observation and not pvalue calculation over a > distribution. You don?t seem to have a spread. Here your code seemed like > it was over all genes(more than 1) vs RG genes(also more than one). But it > is basically an observation of difference of 2 values. So it doesn?t need > to calculate any pvalues. Probability calculation is only needed when you > have distribution of data in each arm to make Ho(null hypothesis) thar > ststes condition 1 vs condition 2 have no difference but when you compute > the distribution, you find a difference that rejects your Null and makes > the alternative hypotheses true. > > Just observed your ?prop? is between only two values. So no reason for > comparing since there is no distribution. > > Just make barplot and compute the Delta that can be difference between > 70.42-7.75 or fold change 70.42/7.75. If they are absolute value you can > also scale them in log scale and do the same. Hope this helps. Good luck. > > Vivek > > On Fri, Sep 27, 2019 at 9:32 PM Ana Marija <sokovic.anamarija at gmail.com> > wrote: > >> Hi Vivek, >> >> Thanks for getting back to me and yes that is what I tried: >> >> library(ggpubr) >> library(ggplot2) >> df <- data.frame("prop" = c(7.75,70.42), "Name" = c("All Genes","RG >> Genes")) >> my_comparisons <- list(c("All Genes","RG Genes")) >> >> p <-ggbarplot(df, x="Name", y="prop",fill="Name",legend ="",color >> "white",palette = "jco",xlab = FALSE,ylab="cis eqtl per gene") >> >> p + stat_compare_means(comparisons=my_comparisons) >> >> I got p value 1, I am wondering does putting here p value makes sense >> because I don't have any distribution, I just have these two numbers >> on y axis: >> "prop" = c(7.75,70.42) >> >> Please advise, >> >> Thanks >> Ana >> >> >> On Fri, Sep 27, 2019 at 11:21 PM Vivek Das <vd4mmind at gmail.com> wrote: >> > >> > You will need to add stat_compare_means. Take a look at here. >> > >> > >> > >> http://www.sthda.com/english/articles/24-ggpubr-publication-ready-plots/76-add-p-values-and-significance-levels-to-ggplots/ >> > >> > library(ggpubr) >> > p + stat_compare_means() >> > >> > Should be fine. >> > >> > Vivek >> > >> > On Fri, Sep 27, 2019 at 7:29 PM Ana Marija <sokovic.anamarija at gmail.com> >> wrote: >> >> >> >> Hi, >> >> >> >> I created a bar plot with this code: >> >> >> >> library(ggplot2) >> >> df <- data.frame("prop" = c(7.75,70.42), "Name" = c("All Genes","RG >> Genes")) >> >> p<-ggplot(data=df, aes(x=Name, y=prop,fill=Name)) + >> >> geom_bar(stat="identity")+ labs(x="", y = "Proportion of cis >> >> EQTLs")+ scale_fill_brewer(palette="Greens") + >> >> theme_minimal()+theme(legend.position = "none") >> >> p >> >> >> >> What do I need to change in my plot so that I have plot with p value >> >> shown on the attached figure? >> >> >> >> Thanks >> >> Ana >> >> ______________________________________________ >> >> 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. >> > >> > -- >> > ---------------------------------------------------------- >> > >> > Vivek Das, PhD >> > -- > ---------------------------------------------------------- > > Vivek Das, PhD >[[alternative HTML version deleted]]