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:
- Display two groups as data points, two groups as confidence ellipses
- 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).
the saved png looks like this.
CodePudding user response：
thank you very much for your response. Thanks to your help, and with some adaptation, I finally got almost the desired result, but there is still some stuff I don't understand.
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 |> mutate(Run_type = c(
rep("MAG", 10), rep("PMAG", 10),
rep("MAG", 10), rep("PMAG", 10)
))
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")
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.