How to display a data group as points and another one as confidence ellipse? Issues with ggplot and ggsave

Question

I am new to R, and I am trying to generate scatter plots with two variables, with the values of each variable grouped into 4 classes.

In particular, I am trying to achieve the following:

1. Display two groups as data points, two groups as confidence ellipses
2. Generate and save scatter plots having the same dimensions in term of plot frame size and plot area (i.e., x-axis long 8 cm, y-axis long 6 cm.).

Below you can find a reproducible version (you just need to define the output for the png file) of the code that works, but it shows data points and confidence ellipses for all data:

library(ggplot2)

out_path = YOUR OUTPUT DIRECTORY

#data frame
gr1 <- (rep(paste('B-12-B-002'), 10))
gr2 <- (rep(paste('B-12-M-03'), 10))
gr3 <-  (rep(paste('b-b-d-3'), 10))
gr4 <-  (rep(paste('h-12-b-01'), 10))

Run_type <- c(gr1,gr2,gr3,gr4)

axial_ratio <- runif(40,0,1) 
Solidity <- runif(40,0,1)
Convexity <- runif(40,0,1)

sel_data_all <- data.frame(Run_type,axial_ratio,Solidity,Convexity)
fill_colors <- c('red','blue','green','orange');

#Plot

one_plot = ggplot(sel_data_all,aes(x = axial_ratio,y = Solidity))+         
  geom_point(aes(x = axial_ratio,y = Solidity, fill = Run_type, shape = Run_type), color = "black", stroke = 1, 
             size = 5, alpha = 0.4)+
  stat_ellipse(data = sel_data_all, aes(x = axial_ratio, y = Solidity, fill = Run_type,colour=Run_type),geom = "polygon",alpha = 0.4,type = "norm",level = 0.6, 
               show.legend = FALSE) +  #, group=Run_type , data = subset(sel_data_all, Run_type %in% leg_keys_man[1:7]),
  scale_shape_manual(values=c(21,21,23,23))+ 
  scale_fill_manual(values = fill_colors)+
  scale_color_manual(values = fill_colors)+
  coord_fixed(ratio = 1)+
  theme(legend.position="top", # write 'none' to hide the legend
        legend.key = element_rect(fill = "white"), # Set background of the points in the legend
        legend.title = element_blank(), # Remove legend title
        
        panel.background=element_rect(fill = "white", colour="black"),
        panel.grid.major=element_line(colour="lightgrey"),
        panel.grid.minor=element_line(colour="lightgrey"),
        axis.title.x = element_text(margin = margin(t = 10), size = 12,face = "bold"), # margin = margin(t = 10) vjust = 0
        axis.title.y = element_text(margin = margin(r = 10), size = 12,face = "bold"), # margin = margin(r = 10) vjust = 2
        axis.text = element_text(color = "black", size = 10), # To hide the text from a specific axis do: axis.text.y = element_blank()
        axis.ticks.length=unit(-0.15, "cm"), # To hide the ticks from a specific axis do: axis.ticks.y = element_blank()
        #plot.margin = margin(t = 0, r = 1, b = 0.5, l = 0.5, unit = "cm"), # define margine of the plot frame t = top, r = right, b = bottom,  l = left
  )
  #expand_limits(x = 0, y = 0)+ #Force the origin of the plot to 0
  #xlim(c(0,1))+
  #ylim(c(0,1)) # or xlim, limit the axis to the values defined

show(one_plot)

# Save plots 
ggsave(
  filename=paste("Axial_ratio","_vs_","Solidity",".png",sep=""),
  plot = one_plot,
  device = "png",
  path = out_path,
  scale = 1,
  width = 8, # Refers to the plot frame, not the area
  height = 6, # Refers to the plot frame, not the area
  units = "cm",
  dpi = 300,
  limitsize = FALSE,
  bg = "white")

Unfortunately, after several days of trying and reading the R documentation and forums, I cannot achieve this.

For the first task, I tried subsetting the data by modifying the geom_point and stat_ellipse functions,

  geom_point(data = subset(sel_data_all, Run_type %in% c('B-12-B-002','B-12-M-03')),aes(x = axial_ratio,y = Solidity, fill = Run_type, shape = Run_type), color = "black", stroke = 1, 
             size = 5, alpha = 0.4)+ #
  stat_ellipse(data = subset(sel_data_all, Run_type %in% c('b-b-d-3','h-12-b-01')), aes(x = axial_ratio, y = Solidity, fill = Run_type,colour=Run_type),geom = "polygon",alpha = 0.4,type = "norm",level = 0.6, 
               show.legend = FALSE) +  #

but I end up with a duplicate of the legend (in grey colour).

Like this.

For my second issue, with the working version of the script at the top of the message,

Here is the plot that shows in the "Plots" window in RStudio:

But this is what is saved in the output directory.

A final note about the second issue: the script presented here is actually inserted in a for loop that generates multiple scatter plots made by unique pairs of two variables, and the data frame provided here is only partial, to make it easier for you to help. Unfortunately, this is what ggsave generates:

axial ratio vs convexity

ves_pct vs axial ratio

Can anybody help?

Thank you in advance to everyone!

EDIT:

So, thanks to MarBlo (which I thank a lot), I managed to get almost what I want, but there is still yet something I cannot figure out.

This is the last version of the code, with some adaptation to better fit the reasoning:

          library(tidyverse)

          set.seed(123)
          gr1 <- (rep(paste("B-12-B-002"), 10))
          gr2 <- (rep(paste("B-12-M-03"), 10))
          gr3 <- (rep(paste("b-b-d-3"), 10))
          gr4 <- (rep(paste("h-12-b-01"), 10))

          Sample_ID <- c(gr1, gr2, gr3, gr4)

          axial_ratio <- runif(40, 0, 1)
          Solidity <- runif(40, 0, 1)
          Convexity <- runif(40, 0, 1)

          sel_data_all <- data.frame(Sample_ID, axial_ratio, Solidity, Convexity)
          fill_colors <- c("#5bd9ca",
          "#1e99d6","#1e49d6","#f2581b80","#e8811280","#e3311280","#fc000080")

          sel_data_all <- sel_data_all |> add_column(Run_type = c(
            rep("MAG", 10), rep("PMAG", 10),
            rep("MAG", 10), rep("PMAG", 10)),   .before = "Sample_ID")
          
          one_plot = ggplot( 

          data = sel_data_all |> dplyr::filter(Run_type == "PMAG"),
          aes(x = axial_ratio, y = Solidity)
        ) +
        
        # CONFIDENCE ELLIPSE
        stat_ellipse(
          data = sel_data_all |> dplyr::filter(Run_type == "MAG"),
          aes(x = axial_ratio, y = Solidity,
              fill = Sample_ID),
          geom = "polygon", type = "norm", 
          level = 0.6,
          colour = 'white', # ellipse border
        ) +
        
        # DATA POINTS
        geom_point(aes(colour = Sample_ID, 
                       shape = Sample_ID),
                   stroke = 0.5,
                   size = 3,
        ) +
        
        scale_color_manual(values = fill_colors[1:3]) + # of Data points
        scale_shape_manual(values = c(21, 21, 23, 23,21,23,22)) + # of data points
        scale_fill_manual(values = fill_colors[4:7]) + # of ellipses
        coord_cartesian(xlim=c(0,1))+
        #scale_x_continuous(expand = expansion(mult = c(0.001, 0.05)))+           
        coord_cartesian(ylim=c(0,1))+           
        #scale_y_continuous(expand = expansion(mult = c(0.001, 0.05)))+
        # Theme
        theme(
          legend.position = "top",
          legend.key.size = unit(5, 'mm'), #change legend key size
          # legend.key.height = unit(1, 'cm'), #change legend key height
          # legend.key.width = unit(1, 'cm'), #change legend key width
          legend.text = element_text(size=8),
          legend.key = element_rect(fill = "white", colour = 'white'),
          legend.background = element_rect(fill = "transparent"),
          legend.title = element_blank(),
          panel.background = element_rect(fill = "white", colour = "black"),
          panel.grid.major = element_line(colour = "lightgrey"),
          panel.grid.minor = element_line(colour = "lightgrey"),
          axis.title.x = element_text(vjust = -1, size = 12, face = "bold"),
          axis.title.y = element_text(vjust = 4, size = 12, face = "bold"),
          axis.text = element_text(color = "black", size = 10),
          axis.ticks.length = unit(-0.15, "cm"),
          plot.margin = margin(t = 2,  # Top margin
                               r = 4,  # Right margin
                               b = 4,  # Bottom margin
                               l = 4, # Left margin
                               unit = "mm"),
        )+
        guides(colour = guide_legend(nrow=2, byrow=TRUE)+
        coord_fixed(ratio = 1))
              ggsave(
            filename=paste("snap",".png",sep=""),
            plot = one_plot,
            device = "png",
            path = here::here(),
            width = 8, # Refers to the plot frame, not the area
            height = 8, # Refers to the plot frame, not the area
            units = "cm",
            #dpi = 300,
            #limitsize = FALSE,
            bg = "white")


    

Here is the saved plot

What I need, are the data points filled with the colour currently used for their border, and the border of all data points in black.

I tried to move around the aesthetics, but I ended up with the duplicate legend and more confusion.

Thanks in advance again for your help.

Answer 1

I have taken your data and added a variable called group which makes filtering in ggplot easier.

If you define x and y in ggplot(..,aes()) you do not have to define it again in geom_point. In geom_point you give already a color to Run_type , the variable from which the legend should be made up. Because you use in geom_ellipse a different subset of the DF the legend would be updated and make again 4 legend entries instead of 2 for the variables only. color = Run_type can therefore be skipped.

I have added set.seed() which ensures that results are being comparable, although random numbers are generated for making up the DF.

library(tidyverse)

set.seed(123)
gr1 <- (rep(paste("B-12-B-002"), 10))
gr2 <- (rep(paste("B-12-M-03"), 10))
gr3 <- (rep(paste("b-b-d-3"), 10))
gr4 <- (rep(paste("h-12-b-01"), 10))

Run_type <- c(gr1, gr2, gr3, gr4)

axial_ratio <- runif(40, 0, 1)
Solidity <- runif(40, 0, 1)
Convexity <- runif(40, 0, 1)

sel_data_all <- data.frame(Run_type, axial_ratio, Solidity, Convexity)
fill_colors <- c("red", "blue", "green", "orange")

df <- sel_data_all |> mutate(group = c(
  rep("Data", 10), rep("Conf", 10),
  rep("Data", 10), rep("Conf", 10)
))

ggplot(
  data = df |> dplyr::filter(group == "Data"),
  aes(x = axial_ratio, y = Solidity)
) +
  geom_point(aes(color = Run_type, shape = Run_type),
    stroke = 1,
    size = 5, alpha = 0.4
  ) +
  stat_ellipse(
    data = df |> dplyr::filter(group != "Data"),
    aes(
      x = axial_ratio, y = Solidity,
      fill = Run_type
    ),
    geom = "polygon", alpha = 0.4, type = "norm", level = 0.6,
    show.legend = FALSE
  ) +
  scale_shape_manual(values = c(21, 21, 23, 23)) +
  scale_fill_manual(values = fill_colors) +
  scale_color_manual(values = fill_colors) +
  coord_fixed(ratio = 1) +
  theme(
    legend.position = "top",
    legend.key = element_rect(fill = "white"),
    legend.title = element_blank(),
    panel.background = element_rect(fill = "white", colour = "black"),
    panel.grid.major = element_line(colour = "lightgrey"),
    panel.grid.minor = element_line(colour = "lightgrey"),
    axis.title.x = element_text(margin = margin(t = 10), size = 12, face = "bold"),
    axis.title.y = element_text(margin = margin(r = 10), size = 12, face = "bold"),
    axis.text = element_text(color = "black", size = 10),
    axis.ticks.length = unit(-0.15, "cm"),
  )

The plot was then saved with equal width and height.

ggsave(
  filename=paste("Axial_ratio","_vs_","Solidity",".png",sep=""),
  plot = last_plot(),
  device = "png",
  path = here::here(),
  width = 8, # Refers to the plot frame, not the area
  height = 8, # Refers to the plot frame, not the area
  units = "cm",
  #dpi = 300,
  #limitsize = FALSE,
  bg = "white")

the saved png looks like this.

---

NEW EDIT

My understanding now is that you want two colors for geom_points and 2 different colors for stat_ellipse.

So the following will show a new attempt. If this is the right answer, I will erase most from above, to make this post better readable.

The ggsave -issue I regard as solved.

I have defined two different color-sets; one for geom_point and one for stat_ellipse. (There are 3 and 4 colors defined, although later in scale_color_manual and scale_fill_manual only 2 colors are needed.)

As for both geom_point and stat_ellipse a different DF is used, ggplot is called without any data or aes. Both will be defined individually when geom_point and stat_ellipse are called.

For stat_ellipse fill is used and for geom_point color is used as aes.

If you want to leave the one or the other legend out, you may use show.legend = F in the respective geom.

xlim and ylim define axis limits.

guides() and theme_bw() make sure that the dark background of legend.key is erased.

I have tried to make the theme aa bit more concise.

library(tidyverse)

set.seed(123)
gr1 <- (rep(paste("B-12-B-002"), 10))
gr2 <- (rep(paste("B-12-M-03"), 10))
gr3 <- (rep(paste("b-b-d-3"), 10))
gr4 <- (rep(paste("h-12-b-01"), 10))

Sample_ID <- c(gr1, gr2, gr3, gr4)

axial_ratio <- runif(40, 0, 1)
Solidity <- runif(40, 0, 1)
Convexity <- runif(40, 0, 1)

sel_data_all <- data.frame(Sample_ID, axial_ratio, Solidity, Convexity)
fill_colors_points <- c("#5bd9ca", "#1e99d6", "#1e49d6")
fill_colors_ellipse <- c("#f2581b80", "#e8811280", "#e3311280", "#fc000080")

sel_data_all <- sel_data_all |> mutate(Run_type = c(
  rep("MAG", 10), rep("PMAG", 10),
  rep("MAG", 10), rep("PMAG", 10)
))

ggplot() +
  stat_ellipse(
    data = sel_data_all |> dplyr::filter(Run_type == "MAG"),
    aes(
      x = axial_ratio, y = Solidity,
      fill = Sample_ID
    ),
    geom = "polygon", type = "norm",
    level = 0.6, show.legend = T
  ) +
  geom_point(
    data = sel_data_all |> dplyr::filter(Run_type == "PMAG"),
    aes(
      x = axial_ratio, y = Solidity,
      color = Sample_ID,
      shape = Sample_ID
    ),
    stroke = 0.5, size = 3,
  ) +
  scale_color_manual(values = fill_colors_points[1:2]) + # of Data points
  scale_fill_manual(values = fill_colors_ellipse[1:2]) + # of ellipses
  xlim(0,1) + ylim(0,1) +
  guides(color = guide_legend(override.aes = list(fill = NA))) +
  theme_bw() +
  theme(
    legend.position = "top",
    legend.key.size = unit(5, "mm"), # change legend key size
    legend.text = element_text(size = 8),
    legend.title = element_blank(),
    panel.background = element_rect(fill = "white", colour = "black"),
    panel.grid = element_line(colour = "lightgrey"),
    axis.title.x = element_text(vjust = -1, size = 12, face = "bold"),
    axis.title.y = element_text(vjust = 4, size = 12, face = "bold"),
    axis.text = element_text(color = "black", size = 10),
    axis.ticks.length = unit(-0.15, "cm"),
  ) +
  coord_fixed(ratio = 1)