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How to adjust and align timepoints on x-axis in the ggplot2

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 r line plot x-axis data frame
• 5,971 views • link
updated by zx8754 zx8754 • written by mohammedtoufiq91 mohammedtoufiq91

Can you post a snippet of the data used to generate that graph? For such an issue a reproducible example is required to properly troubleshoot.

• 0 views • link
written by Mark Mark

Hello mohammedtoufiq91!

It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/126702/

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

• 0 views • link
written by ATpoint ATpoint

@ ATpoint,

Apologies for the confusion. This would not be repeated going forward.

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written by mohammedtoufiq91 mohammedtoufiq91

2 answers

We need to create data for dashed lines, then plot, see example, based on your data. I subsetted it for one facet for simplicity.

library(ggplot2)
library(dplyr)

# example data for one facet
Test_v1_ID$Timepoints <- factor(as.numeric(Test_v1_ID$Timepoints), levels = 1:20, labels = paste0("T", 1:20))
Test_v1_ID$value <- as.numeric(Test_v1_ID$value)
d <- Test_v1_ID[ Test_v1_ID$X12 == "M10.1", ]

# data for dashed lines
dash <- d %>% 
  arrange(Genes, Timepoints) %>% 
  group_by(Genes) %>% 
  mutate(x1 = if_else( is.na(value), lag(Timepoints), factor(NA)),
         x2 = if_else( is.na(value), lead(Timepoints), factor(NA)),
         y1 = if_else( is.na(value), lag(value), NA_real_),
         y2 = if_else( is.na(value), lead(value), NA_real_)) %>% 
  filter(!is.na(y1) & !is.na(y2))

# plot as before, and add dashed lines as segments
ggplot(d, aes(x = Timepoints, y = value, group = Genes, col = Genes)) + 
  geom_point() + 
  geom_line() +
  geom_segment(aes(x = x1, xend = x2, 
                   y = y1, yend = y2 ), data = dash, linetype = "dashed")
• 0 views • link
written by zx8754 zx8754

Hi @zx8754,

I was trying a test run with your R code to understand further, however I keep getting the syntax errors. Am I missing something here.

dash <- d %>% 
  arrange(Genes, Timepoints) %>% 
  group_by(Genes) %>% 
  mutate(x1 = if_elseis.na(value), lag(Timepoints), factor(NA)),
x2 = if_elseis.na(value), lead(Timepoints), factor(NA)),
y1 = if_elseis.na(value), lag(value), NA_real_),
y2 = if_elseis.na(value), lead(value), NA_real_)) %>% 
  filter(!is.na(y1) & !is.na(y2))


dash <- d %>% 
+   arrange(Genes, Timepoints) %>% 
+   group_by(Genes) %>% 
+   mutate(x1 = if_elseis.na(value), lag(Timepoints), factor(NA)),
Error: unexpected ',' in:
"  group_by(Genes) %>% 
  mutate(x1 = if_elseis.na(value), lag(Timepoints), factor(NA)),"
> x2 = if_elseis.na(value), lead(Timepoints), factor(NA)),
Error: unexpected ',' in "x2 = if_elseis.na(value),"
> y1 = if_elseis.na(value), lag(value), NA_real_),
Error: unexpected ',' in "y1 = if_elseis.na(value),"
> y2 = if_elseis.na(value), lead(value), NA_real_)) %>% 
Error: unexpected ',' in "y2 = if_elseis.na(value),"
>   filter(!is.na(y1) & !is.na(y2))
Error in filter(!is.na(y1) & !is.na(y2)) : object 'y1' not found
> 




str(d)
'data.frame':   44 obs. of  4 variables:
 $ Genes     : Factor w/ 8 levels "Gene_A","Gene_B",..: 1 1 1 1 1 1 1 1 1 1 ...
 $ Timepoints: Factor w/ 20 levels "T1","T2","T3",..: 1 2 8 9 10 11 12 16 17 18 ...
 $ value     : num  -1.556 -3.085 -0.721 -0.901 NA ...
 $ X12       : Factor w/ 2 levels "M10.1","M10.2": 1 1 1 1 1 1 1 1 1 1 ...
  ..- attr(*, "names")= chr  "Gene_A" "Gene_A" "Gene_A" "Gene_A" ...
• 0 views • link
written by mohammedtoufiq91 mohammedtoufiq91

Try again.

(biostars website sometimes doesn't render code properly, and some parenthesis disappear, should be ok, now.)

• 0 views • link
written by zx8754 zx8754

@ zx8754 ,

Excellent. Looks great! Thank you.

In my case, I should specify each ID manually as I have 100 of them as below

d <- Test_v1_ID[ Test_v1_ID$X12 == "M10.1", "M10.2", "M10.3", "M10.4", "M10.9", ......... ]

or just any easier method?

• 0 views • link
written by mohammedtoufiq91 mohammedtoufiq91

We will need to use loops.

  • Please avoid asking new questions in the comments, if it is a new question then post a question.
  • Try searching the webs for simple R problems.
• 0 views • link
written by zx8754 zx8754

@ zx8754 ,

Thank you very much for the assistance.

• 0 views • link
written by mohammedtoufiq91 mohammedtoufiq91

Please provide example data.

Just guessing try to change your timepoints into factors, something like:

B1_Patient_Module_ID_sorted$Timepoints <- factor(B1_Patient_Module_ID_sorted$Timepoints,
                                                 levels = 1:20,
                                                 labels = paste0("T", 1:20))

Then we do not need to define the scale_x_discrete(...).

• 0 views • link
written by zx8754 zx8754

@ zx8754,

Excellent. This fixed the issue.

Another question, as shown in the figure timepoint T10, there is no data point which is because of the missing values for that particular timepoint, is there a way to display or represent it by dotted line as there are many such line plots or should it removed for better representation.. For instance, in the Complexheatmap or pheatmap, we say na_col = grey for missing values.

• 0 views • link
written by mohammedtoufiq91 mohammedtoufiq91

Yes, it is possible.

Provide example data

• 0 views • link
written by zx8754 zx8754

@ zx8754 ,

thank you. Here is the data.

dput(Test_v1_ID)
structure(list(Genes = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 
4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 
6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 
7L, 7L, 7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 
8L), .Label = c("Gene_A", "Gene_B", "Gene_C", "Gene_D", "Gene_D.1", 
"Gene_E", "Gene_F", "Gene_G"), class = "factor"), Timepoints = c("1", 
"2", "8", "9", "10", "11", "12", "16", "17", "18", "19", "1", 
"2", "8", "9", "10", "11", "12", "16", "17", "18", "19", "1", 
"2", "8", "9", "10", "11", "12", "16", "17", "18", "19", "1", 
"2", "8", "9", "10", "11", "12", "16", "17", "18", "19", "1", 
"2", "8", "9", "10", "11", "12", "16", "17", "18", "19", "1", 
"2", "8", "9", "10", "11", "12", "16", "17", "18", "19", "1", 
"2", "8", "9", "10", "11", "12", "16", "17", "18", "19", "1", 
"2", "8", "9", "10", "11", "12", "16", "17", "18", "19"), value = c("-1.55598", 
"-3.08452", "-0.720558", "-0.901471", NA, "-1.73362", "-1.27953", 
"0.147734", "-0.31916", "-0.48834", "-1.70071", NA, NA, NA, NA, 
NA, NA, NA, NA, "-17.0921", NA, NA, "-1.34066", "-3.05158", "-0.359577", 
"-0.921044", NA, "-1.71127", "-0.954832", "-0.44804", "-0.58607", 
"0.151555", "-0.656842", "-4.6299", "-5.97264", "-4.11533", "-4.24868", 
NA, "-4.26154", "-3.52369", "-2.58611", "-2.98512", "-2.37213", 
"-3.57149", "-2.05066", "-0.657222", "-1.40576", "-2.29293", 
"-0.509917", "-1.68802", NA, "-1.85783", "-1.9242", NA, "-2.33469", 
"-8.35787", "-9.52402", "-9.55285", "-9.5344", "-9.23144", "-9.94065", 
NA, "-8.96788", "-9.01785", "-9.17554", "-9.90749", "-2.06287", 
"-0.846725", "-1.08125", "-1.7152", "-2.01096", "-2.07493", NA, 
"-1.41699", "-1.471", NA, "-1.67149", "-3.83545", "-1.19723", 
"-1.78817", "-1.78302", NA, "-1.11688", NA, "-1.88749", "-2.20363", 
NA, "-1.79198"), X12 = structure(c(Gene_A = 1L, Gene_A = 1L, 
Gene_A = 1L, Gene_A = 1L, Gene_A = 1L, Gene_A = 1L, Gene_A = 1L, 
Gene_A = 1L, Gene_A = 1L, Gene_A = 1L, Gene_A = 1L, Gene_B = 1L, 
Gene_B = 1L, Gene_B = 1L, Gene_B = 1L, Gene_B = 1L, Gene_B = 1L, 
Gene_B = 1L, Gene_B = 1L, Gene_B = 1L, Gene_B = 1L, Gene_B = 1L, 
Gene_C = 1L, Gene_C = 1L, Gene_C = 1L, Gene_C = 1L, Gene_C = 1L, 
Gene_C = 1L, Gene_C = 1L, Gene_C = 1L, Gene_C = 1L, Gene_C = 1L, 
Gene_C = 1L, Gene_D = 1L, Gene_D = 1L, Gene_D = 1L, Gene_D = 1L, 
Gene_D = 1L, Gene_D = 1L, Gene_D = 1L, Gene_D = 1L, Gene_D = 1L, 
Gene_D = 1L, Gene_D = 1L, Gene_D.1 = 2L, Gene_D.1 = 2L, Gene_D.1 = 2L, 
Gene_D.1 = 2L, Gene_D.1 = 2L, Gene_D.1 = 2L, Gene_D.1 = 2L, Gene_D.1 = 2L, 
Gene_D.1 = 2L, Gene_D.1 = 2L, Gene_D.1 = 2L, Gene_E = 2L, Gene_E = 2L, 
Gene_E = 2L, Gene_E = 2L, Gene_E = 2L, Gene_E = 2L, Gene_E = 2L, 
Gene_E = 2L, Gene_E = 2L, Gene_E = 2L, Gene_E = 2L, Gene_F = 2L, 
Gene_F = 2L, Gene_F = 2L, Gene_F = 2L, Gene_F = 2L, Gene_F = 2L, 
Gene_F = 2L, Gene_F = 2L, Gene_F = 2L, Gene_F = 2L, Gene_F = 2L, 
Gene_G = 2L, Gene_G = 2L, Gene_G = 2L, Gene_G = 2L, Gene_G = 2L, 
Gene_G = 2L, Gene_G = 2L, Gene_G = 2L, Gene_G = 2L, Gene_G = 2L, 
Gene_G = 2L), .Label = c("M10.1", "M10.2"), class = "factor")), row.names = c(NA, 
-88L), class = "data.frame")
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written by mohammedtoufiq91 mohammedtoufiq91

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