Question: Reproducing this radar plot in r
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gravatar for A
11 weeks ago by
A3.9k
A3.9k wrote:

Hello

I have two groups of patients; Responders for a drug and non-responders. For each group I looked for disturbed pathways so that pathways are in columns and patients in the rows

> dput(head(responders[1:2,]))
structure(list(Samples = c("LP6008460.DNA_A04", "s30"), BER = c(0L, 
0L), WNT = 0:1, CR = c(0L, 0L), CPF = c(0L, 0L), TM = c(0L, 0L
), HR = c(0L, 0L), FA = c(0L, 0L), RTK.RAS = c(1L, 1L), CC = c(1L, 
1L), p53 = c(1L, 1L), NOTCH = c(0L, 0L), Hippo = 0:1, PI3K = 0:1, 
    NER = c(0L, 0L), NHEJ = c(0L, 0L), MMR = c(0L, 0L), MYC = c(0L, 
    0L), CS = c(0L, 0L), TLS = c(0L, 0L), UR = c(0L, 0L), TGF.Beta = 1:0, 
    OD = c(0L, 0L), Response = c("Responder", "Responder")), row.names = 1:2, class = "data.frame")
> 


> dput(head(nonresponders[1:2,]))
structure(list(Samples = c("LP6008031.DNA_B02", "LP6005500.DNA_H03"
), BER = 1:0, WNT = 0:1, CR = c(0L, 0L), CPF = c(1L, 1L), TM = c(0L, 
0L), HR = 1:0, FA = c(0L, 0L), RTK.RAS = c(1L, 1L), CC = c(1L, 
1L), p53 = c(1L, 1L), NOTCH = c(1L, 1L), Hippo = c(0L, 0L), PI3K = c(1L, 
1L), NER = 0:1, NHEJ = 1:0, MMR = c(0L, 0L), MYC = 1:0, CS = c(0L, 
0L), TLS = 1:0, UR = 1:0, TGF.Beta = 0:1, OD = c(0L, 0L), Response = c("Non-Responder", 
"Non-Responder")), row.names = 1:2, class = "data.frame")
>

I want to have such a plot, but each pathway is a chunk of this plot and responders and non-responders are two side-by-side bars for each pathway

enter image description here

For example here each bacteria could be a different pathway

The Python script for this figure is here https://docs.bokeh.org/en/latest/docs/gallery/burtin.html but I don't know how to use Python

R • 231 views
ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by A3.9k
1

Can you edit your posts to include the results of dput(head(responders[1:2,])) and dput(head(nonresponders[1:2,]))?

ADD REPLYlink written 11 weeks ago by rpolicastro3.2k

Thank you so much. I have edited the main post

ADD REPLYlink written 11 weeks ago by A3.9k

I have found this code to give a polar plot but I don't know how to combine two groups in that with different colours

 require(gdata)
    library(reshape2)
    library(ggplot2)
    library(fmsb)
    library(plotrix)
    library(RColorBrewer)
    library(gplots)
    library(NMF)
    rownames(responders)=responders[,1]
    responders=responders[,-1]
   responders=responders[,-23]
    coordpos<-seq(0,350,by=360/(length(colnames(responders))))
    pdf(paste(getwd(),"pdf.pdf",sep=""))
    polar.plot(colSums(responders)/nrow(responders),coordpos,main="Responders",
               start=90,clockwise=TRUE,lwd=5,line.col="#43a2ca",rp.type="p",
               labels=names(colSums(responders)),label.pos=coordpos,radial.lim=c(0,1))
    dev.off()

This gives polar plot for one group. Do you know how to combine the second group in the plot with different colour?

enter image description here

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by A3.9k
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