How to adjust and align timepoints on x-axis in the ggplot2
2
0
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5.0 years ago

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 • 4.4k views
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1
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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.

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0
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@ ATpoint,

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

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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.

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3
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5.0 years ago
zx8754 12k

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")
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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" ...
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1
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Try again.

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

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0
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@ 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?

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1
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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.
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0
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@ zx8754 ,

Thank you very much for the assistance.

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1
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5.0 years ago
zx8754 12k

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(...).
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@ 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.

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2
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Yes, it is possible.

Provide example data

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@ 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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