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