Enhancing Visualizations: Manipulating Color and Shape in R with Two Variables

Enhancing Visualizations: Manipulating Color and Shape in R with Two Variables

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I have one dataset as below. 

library(readr)
github="https://raw.githubusercontent.com/agronomy4future/raw_data_practice/main/genotype_transgenic_line_with_fertilizer.csv"
dataA= data.frame(read_csv(url(github), show_col_types= FALSE))

dataA
         genotype plot resistance fertilizer   GN   AGW
1             cv1    1         no        150 1310 33.15
2             cv1    1         no          0 1168 25.07
3             cv1    1         no        200  570 36.04
4             cv2    1         no        150 1120 53.05
5             cv2    1         no          0 1230 26.71
6             cv2    1         no        200  795 37.75
7             cv3    1        yes        150 2013 27.51
8             cv3    1        yes          0 2183 24.61
9             cv3    1        yes        200 1034 36.53
10            cv4    1         no        150 2451 31.58
.
.
.

Now, I’ll create a regression graph between grain number (GN) and average grain weight (AGW).

library(ggplot2)
FIG1=ggplot(data=dataA, aes(x=GN, y=AGW))+
  geom_point(aes(fill=genotype, shape=genotype), color= "black", size= 5) +
  geom_smooth(method='lm', linetype=1, se=FALSE, color="red", formula=y~x, size=0.5) +
  scale_fill_manual(values=c("blue","red","orange","purple","green","black"))+
  scale_shape_manual(values=rep(c(21),6))+
  scale_x_continuous(breaks=seq(0,5000,1000), limits = c(0,5000)) +
  scale_y_continuous(breaks=seq(0,80,20), limits = c(0,80)) +
  labs(x="Grain number per panicle", y="Average grain weight (mg) per panicle") +
  theme_classic(base_size=18, base_family="serif")+
  theme(legend.position=c(0.8,0.8),
        legend.title=element_blank(),
        legend.key=element_rect(color="white", fill="white"),
        legend.text=element_text(family="serif", face="plain",
                                 size=13, color= "Black"),
        legend.background=element_rect(fill="white"),
        axis.line=element_line(linewidth=0.5, colour="black"),
        strip.background=element_rect(color="white", 
                                      linewidth=0.5,linetype="solid"))
FIG1+windows(width=5.5, height=5)
ggsave("C:/Users/Desktop/R_OUTPUT/FIG1.jpg", 
       FIG1, width=5.5*2.54, height=5*2.54, units="cm", dpi=1000)

I distinguished genotypes with different colors, and now I want to differentiate resistance (yes and no) using distinct shapes. Therefore, I’ll be changing the shape representation from genotype to resistance.

library(ggplot2)
FIG2=ggplot(data=dataA, aes(x=GN, y=AGW))+
  geom_point(aes(fill=genotype, shape=resistance), color= "black", size= 5) +
  geom_smooth(method='lm', linetype=1, se=FALSE, color="red", formula=y~x, size=0.5) +
  scale_fill_manual(values=c("blue","red","orange","purple","green","black"))+
  scale_shape_manual(values=c(21,22)) +
  scale_x_continuous(breaks=seq(0,5000,1000), limits = c(0,5000)) +
  scale_y_continuous(breaks=seq(0,80,20), limits = c(0,80)) +
  labs(x="Grain number per panicle", y="Average grain weight (mg) per panicle") +
  theme_classic(base_size=18, base_family="serif")+
  theme(legend.position=c(0.8,0.8),
        legend.title=element_blank(),
        legend.key=element_rect(color="white", fill="white"),
        legend.text=element_text(family="serif", face="plain",
                                 size=13, color= "Black"),
        legend.background=element_rect(fill="white"),
        axis.line=element_line(linewidth=0.5, colour="black"),
        strip.background=element_rect(color="white", 
                                      linewidth=0.5,linetype="solid"))
FIG2+windows(width=5.5, height=5)

However, the color is not currently applied to the legend. I aim to apply the provided color to the legend, and additionally, assign colors to represent different levels of resistance.

Here is the solution!!

library(ggplot2)
FIG3=ggplot(data=dataA, aes(x=GN, y=AGW))+
  geom_point(aes(fill=genotype, shape=resistance), color= "black", size= 5) +
  geom_smooth(method='lm', linetype=1, se=FALSE, color="red", formula=y~x, size=0.5) +
scale_fill_manual(values=c("tomato1","tomato3","tomato4","blue","darkblue","black"), 
                  guide=guide_legend(override.aes=list(shape=21))) +
scale_shape_manual(values=c(24,22), 
                   guide=guide_legend(override.aes=list(colour="black"))) + 
  scale_x_continuous(breaks=seq(0,5000,1000), limits = c(0,5000)) +
  scale_y_continuous(breaks=seq(0,80,20), limits = c(0,80)) +
  labs(x="Grain number per panicle", y="Average grain weight (mg) per panicle") +
  theme_classic(base_size=18, base_family="serif")+
  theme(legend.position=c(0.8,0.8),
        legend.title=element_blank(),
        legend.key=element_rect(color="white", fill="white"),
        legend.text=element_text(family="serif", face="plain",
                                 size=13, color= "Black"),
        legend.background=element_rect(fill="white"),
        axis.line=element_line(linewidth=0.5, colour="black"),
        strip.background=element_rect(color="white", 
                                      linewidth=0.5,linetype="solid"))
FIG3+windows(width=5.5, height=5)
ggsave("C:/Users/dream/Desktop/R_OUTPUT/FIG3.jpg", 
       FIG3, width=5.5*2.54, height=5*2.54, units="cm", dpi=1000)

If you want to display two legend horizontally, you can add legend.box="horizontal"

library(ggplot2)
FIG4=ggplot(data=dataA, aes(x=GN, y=AGW))+
  geom_point(aes(fill=genotype, shape=resistance), color= "black", size= 5) +
  geom_smooth(method='lm', linetype=1, se=FALSE, color="red", formula=y~x, size=0.5) +
scale_fill_manual(values=c("tomato1","tomato3","tomato4","blue","darkblue","black"),
                  guide=guide_legend(override.aes=list(shape=21))) +
scale_shape_manual(values=c(24,22), 
                   guide=guide_legend(override.aes=list(colour="black"))) + 
  scale_x_continuous(breaks=seq(0,5000,1000), limits = c(0,5000)) +
  scale_y_continuous(breaks=seq(0,80,20), limits = c(0,80)) +
  labs(x="Grain number per panicle", y="Average grain weight (mg) per panicle") +
  theme_classic(base_size=18, base_family="serif")+
  theme(legend.position=c(0.65,0.8),
        legend.box= "horizontal", 
        legend.title=element_blank(),
        legend.key=element_rect(color="white", fill="white"),
        legend.text=element_text(family="serif", face="plain",
                                 size=13, color= "Black"),
        legend.background=element_rect(fill="white"),
        axis.line=element_line(linewidth=0.5, colour="black"),
        strip.background=element_rect(color="white", 
                                      linewidth=0.5, linetype="solid"))
FIG4+windows(width=5.5, height=5)
ggsave("C:/Users/dream/Desktop/R_OUTPUT/FIG4.jpg", 
       FIG4, width=5.5*2.54, height=5*2.54, units="cm", dpi=1000)
full code; https://github.com/agronomy4future/raw_data_practice/blob/main/different_color_shape_legend

library(readr)
library(ggplot2)

github="https://raw.githubusercontent.com/agronomy4future/raw_data_practice/main/genotype_transgenic_line_with_fertilizer.csv"
dataA= data.frame(read_csv(url(github), show_col_types= FALSE))

FIG4=ggplot(data=dataA, aes(x=GN, y=AGW))+
  geom_point(aes(fill=genotype, shape=resistance), color= "black", size= 5) +
  geom_smooth(method='lm', linetype=1, se=FALSE, color="red", formula=y~x, size=0.5) +
  scale_fill_manual (values=c("tomato1","tomato3","tomato4","blue","darkblue","black"), guide=guide_legend(override.aes=list(shape=21))) +
  scale_shape_manual(values=c(24,22), guide=guide_legend(override.aes=list(colour="black"))) + 
  scale_x_continuous(breaks=seq(0,5000,1000), limits = c(0,5000)) +
  scale_y_continuous(breaks=seq(0,80,20), limits = c(0,80)) +
  labs(x="Grain number per panicle", y="Average grain weight (mg) per panicle") +
  theme_classic(base_size=18, base_family="serif")+
  theme(legend.position=c(0.65,0.8),
        legend.box= "horizontal", 
        legend.title=element_blank(),
        legend.key=element_rect(color="white", fill="white"),
        legend.text=element_text(family="serif", face="plain",
                                 size=13, color= "Black"),
        legend.background=element_rect(fill="white"),
        axis.line=element_line(linewidth=0.5, colour="black"),
        strip.background=element_rect(color="white", 
                                      linewidth=0.5, linetype="solid"))
FIG4+windows(width=5.5, height=5)
ggsave("C:/Users/dream/Desktop/R_OUTPUT/FIG4.jpg", 
       FIG4, width=5.5*2.54, height=5*2.54, units="cm", dpi=1000)

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