How to adjust and align timepoints on x-axis in the ggplot2
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@mohammedtoufiq91-17679
Last seen 7 weeks ago
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Question posted on https://www.biostars.org/p/409725/

Hi,

I am working on the line plot using ggplot2 library. I notice that the data point are not aligned correctly on the x-axis (different timepoints). Below is the code that I ran in R and image of the line plot. In the Image, as shown data point from T5 is aligned on T6 and T20 is not aligned as well. Please let me know how to fix the issue.

Note: Some data points are indeed missing in the middle as they are not present in the dataframe.

str(B1_Patient_Module_ID_sorted)
'data.frame':   5016 obs. of  4 variables:
 $ Genes     : Factor w/ 264 levels "ABHD5","ACOT4",..: 1 2 3 4 5 6 7 8 9 10 ...
 $ Timepoints: num  1 1 1 1 1 1 1 1 1 1 ...
 $ value     : num  -2.05 -8.36 -2.06 -3.84 -6.59 ...
 $ X20       : Factor w/ 66 levels "M10.1","M10.2",..: 53 59 53 53 44 6 29 12 29 19 ...
  ..- attr(*, "names")= chr  "ABHD5" "ACOT4" "ACTN4" "ACTR10" ...


pdf("B1_Module_v3.pdf", 7, 6)
for (i in seq(1, length(unique(B1_Patient_Module_ID_sorted$X20)), 1)) {
  print(ggplot(B1_Patient_Module_ID_sorted[B1_Patient_Module_ID_sorted$X20 %in% levels(B1_Patient_Module_ID_sorted$X20)[i:(i)], ], 
               aes(x =  Timepoints , y = value , group = Genes)) + 
          geom_point() + 
          geom_line(alpha = 1 , aes(col = Genes)) + 
          facet_wrap(~ X20) +
          scale_y_continuous(name = "-Delta Ct")+
          scale_x_discrete(name = "Timepoints", limits=c("1"= "T1", "2" = "T2",  "3" = "T3",  "5"= "T5", "6" = "T6", "7" = "T7", "8"= "T8", "9" = "T9",  "10" = "T10", "11"= "T11", "12" = "T12",  "13" = "T13", "14"= "T14", "15" = "T15", "16" = "T16", "17"= "T17", "18" = "T18", "19" = "T19", "20" = "T20"))+
          theme_classic()+
          theme(legend.position = "right") +
          theme(plot.title = element_text(lineheight=.8,size =14,face = "bold"),
                axis.text.x = element_text(colour="black",size=4.5,angle=0,hjust=0.5,vjust=0.5,face="plain"),
                axis.text.y = element_text(colour="black",size=4,angle=0,hjust=0,vjust=0.5,face="plain"),  
                axis.title.x = element_text(colour="black",size=15,angle=0,hjust=.5,vjust=0,face="plain"),
                axis.title.y = element_text(colour="black",size=14,angle=90,hjust=.5,vjust=.5,face="plain"),
                strip.background = element_blank(),
                legend.position = "right"))
}
dev.off()

Thank you,

Toufiq

ggplot2 line plot x-axis data frame R • 566 views
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Hello mohammedtoufiq91!

It appears that your post has been cross-posted to another site: Please don't cross-post. Also, this isn't a question about BioC packages, so you should just use biostars

This is typically not recommended as it runs the risk of annoying people in both communities.

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