I used the same code to plot my data last week, and got it all right. I updated the data with new rows, so this is the only thing I changed, but then ggplot does not plot the data but a bunch of numbers as shown in the pictures I attached.
I'm sure it is something about how the data is coded, but when it happened last week, what I did was to use as.numeric, and that's it.
**# Read the data
experiment_6 <- read.csv("Data_Experiments.xlsx - experiment_6.csv", header=TRUE)
#clean the irrelevant rows
experiment_6_clean <- experiment_6[-c(1,2), ]
#check if it data.frame
is.data.frame(experiment_6_clean)
#remove Nas from dataset
#experiment_6_clean %>% drop_na()
#select relevant data
experiment_6_clean<- experiment_6_clean[1:517,]
#rename columns
experiment_6_clean<- dplyr::rename(experiment_6_clean,
mean_S_both_Par= X, plusSD_S_both_Par= X.1, minusSD_S_both_Par=X.2,
mean_S_both_Agl=X.3,plusSD_S_both_Agl= X.4, minusSD_S_both_Agl= X.5,
mean_M_both_Par= X.6,plusSD_M_both_Par= X.7, minusSD_M_both_Par= X.8,
mean_M_both_Agl= X.9, plusSD_M_both_Agl= X.10,minusSD_M_both_Agl= X.11,
mean_L_water_Sch= X.12, plusSD_L_water_Sch= X.13, minusSD_L_water_Sch= X.14,
mean_L_both_Sch= X.15, plusSD_L_both_Sch=X.16, minusSD_L_both_Sch= X.17,
Time= X1)
#make all relevant data numeric
Time<- as.numeric(experiment_6_clean$Time)
#small_pots_both_par------4"_2mm_BothSides_Par
mean_S_both_Par<- as.numeric(experiment_6_clean$mean_S_both_Par)
plusSD_S_both_Par<- as.numeric(experiment_6_clean$plusSD_S_both_Par)
minusSD_S_both_Par<- as.numeric(experiment_6_clean$minusSD_S_both_Par)
#small_pots_both_agl---4"_2mm_BothSides_Agl
mean_S_both_Agl<- as.numeric(experiment_6_clean$mean_S_both_Agl)
plusSD_S_both_Agl<- as.numeric(experiment_6_clean$plusSD_S_both_Agl)
minusSD_S_both_Agl<- as.numeric(experiment_6_clean$minusSD_S_both_Agl)
#medium_pots_both_par---6"_2mm_BothSides_Par
mean_M_both_Par<- as.numeric(experiment_6_clean$mean_M_both_Par)
plusSD_M_both_Par<- as.numeric(experiment_6_clean$plusSD_M_both_Par)
minusSD_M_both_Par<- as.numeric(experiment_6_clean$minusSD_M_both_Par)
#medium_pots_both_agl---6"_2mm_BothSides_Agl
mean_M_both_Agl<- as.numeric(experiment_6_clean$mean_M_both_Agl)
plusSD_M_both_Agl<- as.numeric(experiment_6_clean$plusSD_M_both_Agl)
minusSD_M_both_Agl<- as.numeric(experiment_6_clean$minusSD_M_both_Agl)
#large_pots_water_Sch---10"_4mm_WaterSide_Sch
mean_L_water_Sch<- as.numeric(experiment_6_clean$mean_L_water_Sch)
plusSD_L_water_Sch<- as.numeric(experiment_6_clean$plusSD_L_water_Sch)
minusSD_L_water_Sch<- as.numeric(experiment_6_clean$minusSD_L_water_Sch)
#large_pots_both_Sch---10"_5mm_BothSides_Sch
mean_L_both_Sch<- as.numeric(experiment_6_clean$mean_L_both_Sch)
plusSD_L_both_Sch<- as.numeric(experiment_6_clean$plusSD_L_both_Sch)
minusSD_L_both_Sch<- as.numeric(experiment_6_clean$minusSD_L_both_Sch)
experiment_6_clean<- as.data.frame(experiment_6_clean)
#plot
#create key
colors <- c(mean_S_both_Par = "light blue", mean_S_both_Agl = "red", mean_M_both_Par = "orange",
mean_M_both_Agl = "violet", mean_L_water_Sch = "pink", mean_L_both_Sch = "yellow")
#compare all six pots
all_six<- ggplot(experiment_6_clean, aes(x=Time))+
geom_smooth(aes(y=mean_S_both_Par, colour = "mean_S_both_Par"), size = 2, se=TRUE ) +
geom_smooth(aes(y=mean_S_both_Agl, colour = "mean_S_both_Agl"), size = 2, se=TRUE)+
geom_smooth(aes(y=mean_M_both_Par, colour = "mean_M_both_Par"), size = 2, se=TRUE)+
geom_smooth(aes(y=mean_M_both_Agl, colour = "mean_M_both_Agl"),size = 2, se=TRUE )+
geom_smooth(aes(y=mean_L_water_Sch, colour = "mean_L_water_Sch"),size = 2, se=TRUE)+
geom_smooth(aes(y=mean_L_both_Sch,colour = "mean_L_both_Sch"),size = 2, se=TRUE)+
labs(title="Experiment 6", subtitle="All Plants", caption="20 days",
y="Mositure Level", x="Time", color = "Group") +
scale_color_manual(values = colors)+
theme(plot.title=element_text(size=20, face="bold"), axis.text.x=element_text(size=15),
axis.text.y=element_text(size=15))+
coord_cartesian(ylim=c(-100, 150), xlim=c(0, 25))+
theme_bw()
all_six**