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I created a ggplot function to plot groups of data given below (I am sorry, I do not know how to post the data file) enter image description here There are three problems with this graph:

1.The Y-axis title has a superscripted character. Because of this, it cannot be bolded (the same formatting for the x-axis title works)

2.The Legend title is defined as "Group ID". But the code is using the Column Title "GroupID" ignoring the definition. (The code line "scale_fill_discrete("Group ID")" supposed to set the legend title).

3.The width of error bars is not constant, it is changing from point to point (easily noticeable for the green ones)

I appreciate any help to fix these issues.

Code: 

library(ggplot2)

# Colors
Mycolors<- c("blue", "red", "green", "cyan", "orange", "brown", "magenta", "grey", "black")
# Shapes
Myshapes<-c(15:25,0:2)
# Plot position
Mypd <- position_dodge(width = 0.2)

# Read data
mData<-read.csv("F:/user/documents/R/Notebooks/Ggplot/TestData.csv")

pAllGroupData<-function(mData, xLabel, yLabel, gTitle, sTitle, sCaption, yType, gErrType) {

  v <- mData$dMean
  x <- mData$DayNum

    p <- ggplot(data = mData, mapping = aes(x = x, y = v, color = GroupID, shape = GroupID))
    p <- p + geom_line(position = Mypd) +
             geom_point(position = Mypd, size = 4)

  # Plot errorbars  
    if (gErrType == "StdErr") {
      p<- p + geom_errorbar(aes(x = x, ymin = v - mData$dStdErr, ymax = v + mData$dStdErr), width=1.5, position=Mypd)
    } else if (gErrType == "StdDev") {
      p<- p + geom_errorbar(aes(x = x, ymin = v - mData$dStdDev, ymax = v + mData$dStdDev), width=1.5, position=Mypd)
    } else if (gErrType == "IQR")  {
      p<- p + geom_errorbar(aes(x = x, ymin = v - mData$dIQR, ymax = v + mData$dIQR), width=1.5, position=Mypd)
    }

  # Turn Y axis logarithmic and place log ticks
  if (yType == "Log") {
     p<- p + ylim (1, vMax) + # This is to avoid log(0)
      coord_trans(y = "log10") +
      annotation_logticks(sides = "lr", scaled=FALSE)  # ticks are only left and right y axes
  }

  # Plot the graph with theme
  p <- p +
    labs(x = xLabel, y = yLabel, title = gTitle, subtitle = sTitle,  caption = sCaption) +
    # Include origine (0, 0)
    expand_limits(x = 0, y = 0) + 
    # Custom Colors
    scale_colour_manual(values = Mycolors) +
    # Custom Shapes
    scale_shape_manual(values = Myshapes) +
    # Legend Title (not working!)
    scale_fill_discrete("Group ID")

  p <- p + gTheme(p)

  return(p)
}

# Test
p<-pAllGroupData(mData, xLabel = "Days", yLabel = bquote("Volume "~(mm^3)), gTitle = "Study", sTitle = "X", sCaption = "SCaption", yType = "Lin", gErrType = "StdDev")
p

Data:

GroupID DayNum  n   dMean   dMedian dStdDev dStdErr dIQR
Grp1    13  8   207.03  211.45  13.04   4.61    11.73
Grp1    15  8   288.15  274.40  48.98   17.32   33.25
Grp1    18  8   393.50  381.15  63.63   22.50   52.98
Grp1    21  8   507.63  499.80  73.06   25.83   80.88
Grp1    26  8   636.14  614.65  112.53  39.79   206.53
Grp2    13  8   207.05  205.25  41.00   14.50   72.35
Grp2    15  8   142.76  145.60  27.87   9.85    33.70
Grp2    18  8   77.55   82.55   19.44   6.87    22.88
Grp2    21  8   66.38   69.85   20.56   7.27    23.00
Grp2    26  8   67.05   64.20   29.02   10.26   25.48
Grp2    29  8   66.48   63.85   25.95   9.17    19.38
Grp2    33  8   76.96   74.25   25.31   8.95    28.60
Grp3    13  8   207.94  219.65  34.42   12.17   47.18
Grp3    15  8   149.56  155.25  45.74   16.17   70.68
Grp3    18  8   134.83  128.00  59.10   20.90   66.20
Grp3    21  8   164.99  159.40  67.86   23.99   93.63
Grp3    26  8   149.53  160.05  62.48   22.09   100.58
Grp3    29  8   162.21  184.25  61.21   21.64   113.33
Grp3    33  8   177.19  184.00  68.99   24.39   110.35
Grp3    36  8   192.13  160.25  94.93   33.56   122.30
user1046647
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1 Answers1

2

It is advisable to split your question in several posts when you have several problems. Meanwhile here is my attempt to help you:

Problem 1

Replace yLabel = bquote("Volume "~(mm^3)) with yLabel = bquote(bold("Volume " ~ (mm ^ 3))) (note the bold). Kind reminder that this problem was addressed in the past here and also here

Problem 2

You do not use any fill aesthetic, so remove scale_fill_discrete("Group ID"), which has no effect and for each of your aesthetics that you actually use (color and shape), in scale_colour_manual and scale_shape_manual add name = "Group ID" (the desired title of your legend):

scale_colour_manual(name = "Group ID", values = Mycolors) +
scale_shape_manual(name = "Group ID", values = Myshapes)

Problem 3

This seems to have been reported as an issue by some on GitHub, here (the link includes a solution as well)

Similar questions on SO: ggplot2 position_dodge affects error bar width and Width of error bars in ggplot2, both having some answers that you can explore with.

So, you should scale the width of the error bar to the number of row counts for each DayNum. So create a new column in your data.frame, say width like this: 

library(dplyr)

mData <- mData %>%
  group_by(DayNum) %>%
  mutate(width = 1.5 * n())

Then you will have to map this column into the width aesthetic of ggplot while you delete any width attribute from geom_errorbar.

Here is an working example with your data, covering all the 3 problems.

Your data:

mData <- read.table(
  text = "
  GroupID DayNum  n   dMean   dMedian dStdDev dStdErr dIQR
  Grp1    13  8   207.03  211.45  13.04   4.61    11.73
  Grp1    15  8   288.15  274.40  48.98   17.32   33.25
  Grp1    18  8   393.50  381.15  63.63   22.50   52.98
  Grp1    21  8   507.63  499.80  73.06   25.83   80.88
  Grp1    26  8   636.14  614.65  112.53  39.79   206.53
  Grp2    13  8   207.05  205.25  41.00   14.50   72.35
  Grp2    15  8   142.76  145.60  27.87   9.85    33.70
  Grp2    18  8   77.55   82.55   19.44   6.87    22.88
  Grp2    21  8   66.38   69.85   20.56   7.27    23.00
  Grp2    26  8   67.05   64.20   29.02   10.26   25.48
  Grp2    29  8   66.48   63.85   25.95   9.17    19.38
  Grp2    33  8   76.96   74.25   25.31   8.95    28.60
  Grp3    13  8   207.94  219.65  34.42   12.17   47.18
  Grp3    15  8   149.56  155.25  45.74   16.17   70.68
  Grp3    18  8   134.83  128.00  59.10   20.90   66.20
  Grp3    21  8   164.99  159.40  67.86   23.99   93.63
  Grp3    26  8   149.53  160.05  62.48   22.09   100.58
  Grp3    29  8   162.21  184.25  61.21   21.64   113.33
  Grp3    33  8   177.19  184.00  68.99   24.39   110.35
  Grp3    36  8   192.13  160.25  94.93   33.56   122.30",
  header = TRUE
)

An working example:

library(dplyr)
library(ggplot2)

# Solves Problem 3 - create helper column width
mData <- mData %>%
  group_by(DayNum) %>%
  mutate(width = 1.5 * n())

Mypd <- position_dodge(width = 0.2)

ggplot(data = mData, 
       mapping = aes(x = DayNum, 
                     y = dMean, 
                     color = GroupID, 
                     shape = GroupID,
                     width = width)) + # map width column to width aesthetic
  geom_line(position = Mypd) +
  geom_point(position = Mypd, 
             size = 2) +
  # width is inherited from the above mapping, no need to map it again
  geom_errorbar(aes(ymin = dMean - mData$dStdDev, 
                    ymax = dMean + mData$dStdDev), 
                position = Mypd) +
  labs(y = bquote(bold("Volume " ~ (mm ^ 3)))) + # Solves Problem 1
  # Solves Problem 2:
  scale_colour_manual(name = "Group ID", values = c("Grp1" = "blue",
                                                    "Grp2" = "red",
                                                    "Grp3" = "green")) +
  scale_shape_manual(name = "Group ID", values = c("Grp1" = 15,
                                                   "Grp2" = 16,
                                                   "Grp3" = 17)) +
  theme_bw()

enter image description here

Valentin_Ștefan
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