[R] how to add p values to bar plot?

[Vivek Das]

Well that means already a ratio. Could you show me how the data frame looks
like? If they are array of values then you compare the distribution of your
ratios like Ratio1 array from “ (#of EQTLs)/(#of genes)” vs Ratio 2 arrays
of the “same for the other, RG condition”.

ratio1 = c(ratio1Value1, ratio1Value2, ..., ratio1ValueN)
ratio2 = c(ratio2Value1, ratio2Value2, ..., ratio2ValueN)

your code can compare distribution, means & pvalue of these and make
whisker plots and also the pvalues. This is a better way if you can make
your dataframe in that manner to compute and make the plots. Hope this is
clear.

Vivek

On Fri, Sep 27, 2019 at 9:52 PM Ana Marija <sokovic.anamarija using gmail.com>
wrote:

> 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 using 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 using 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 using 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 using 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 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.
>>> >
>>> > --
>>> > ----------------------------------------------------------
>>> >
>>> > Vivek Das, PhD
>>>
>> --
>> ----------------------------------------------------------
>>
>> Vivek Das, PhD
>>
> --
----------------------------------------------------------

Vivek Das, PhD

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