R Notebook

getwd()

[1] "C:/Users/J Lab/Desktop"

setwd("C:/Users/J Lab/Desktop")
list.files(pattern=".csv")

 [1] "20240402_CSHL-15-TEST.csv"                    "cowpea_combining_csv"                        
 [3] "day 1 pot weights - Sheet1.csv"               "Exp_90_Arabidopsis_DUF247_BEFORE_curated.csv"
 [5] "Exp_91_Arabidopsis_DUF247_AFTER_curated.csv"  "gprofiler_results_Mov10oe.csv"               
 [7] "ICPMS_average_HS_20240529.csv"                "ICPMS_curated_HS_20240530.csv"               
 [9] "LncRNA_20201030_meta.csv"                     "multifacet_test.csv"                         
[11] "PhotosynQ_aeroponics_HS_20240313.csv"         "RSA_RNAi_1.csv"                              
[13] "RSA_RNAi_2.csv"                               "RSA_RNAi_3_4.csv"                            
[15] "RSA_RNAi_dufOE_updated.csv"                   "RSA2_improved_tracing.csv"                   
[17] "RSA3_root_tracing_HS.csv"                     "RSA4_20231016_24_HS.csv"                     
[19] "Tray_key_match.csv"                          

aero_ICPMS <- read.csv("ICPMS_curated_HS_20240530.csv")
aero_ICPMS

#Get rid of roots, since most nutrients accumulate in shoot
aero_ICPMS <- subset(aero_ICPMS, aero_ICPMS$Sample != "root")
aero_ICPMS

aero_ICPMS$Treatment2 <- aero_ICPMS$Treatment
unique(aero_ICPMS$Treatment2)

[1] "control" "timed"   "soil"   

aero_ICPMS$Treatment2 <- gsub("control", "aero", aero_ICPMS$Treatment2)
aero_ICPMS$Treatment2 <- gsub("timed", "aero", aero_ICPMS$Treatment2)

library(ggplot2)
library(ggpubr)

Al_errorplot <- ggerrorplot(aero_ICPMS, y="Al", x="Sample", fill="Sample", color = "Treatment",
                                desc_stat = "mean_sd", add="jitter",
                                xlab="", ylab="Amount in 20 mL (mg/L)", main = "Al accumulation in aeroponics vs soil") + theme(axis.text.x = element_text(angle = 90))
Al_errorplot <- Al_errorplot + stat_compare_means(method = "t.test", ref.group = "leaf", label = "p.signif")
Al_errorplot

B_errorplot <- ggerrorplot(aero_ICPMS, y="B", x="Sample", fill="Sample",color = "Treatment",
                                desc_stat = "mean_sd", add="jitter",
                                xlab="", ylab="Amount in 20 mL (mg/L)", main = "B accumulation in aeroponics vs soil") + theme(axis.text.x = element_text(angle = 90))
B_errorplot <- B_errorplot + stat_compare_means(method = "t.test", ref.group = "leaf", label = "p.signif")
B_errorplot

Ca_errorplot <- ggerrorplot(aero_ICPMS, y="Ca", x="Sample", fill="Sample", color = "Treatment",
                                desc_stat = "mean_sd", add="jitter",
                                xlab="", ylab="Amount in 20 mL (mg/L)", main = "Ca accumulation in aeroponics vs soil") + theme(axis.text.x = element_text(angle = 90))
Ca_errorplot <- Ca_errorplot + stat_compare_means(method = "t.test", ref.group = "leaf", label = "p.signif")
Ca_errorplot

Fe_errorplot <- ggerrorplot(aero_ICPMS, y="Fe", x="Sample", fill="Sample", color = "Treatment",
                                desc_stat = "mean_sd", add="jitter",
                                xlab="", ylab="Amount in 20 mL (mg/L)", main = "Fe accumulation in aeroponics vs soil") + theme(axis.text.x = element_text(angle = 90))
Fe_errorplot <- Fe_errorplot + stat_compare_means(method = "t.test", ref.group = "leaf", label = "p.signif")
Fe_errorplot

K_errorplot <- ggerrorplot(aero_ICPMS, y="K", x="Sample", fill="Sample", color = "Treatment",
                                desc_stat = "mean_sd", add="jitter",
                                xlab="", ylab="Amount in 20 mL (mg/L)", main = "K accumulation in aeroponics vs soil") + theme(axis.text.x = element_text(angle = 90))
K_errorplot <- K_errorplot + stat_compare_means(method = "t.test", ref.group = "leaf", label = "p.signif")
K_errorplot

Mg_errorplot <- ggerrorplot(aero_ICPMS, y="Mg", x="Sample", fill="Sample", color = "Treatment",
                                desc_stat = "mean_sd", add="jitter",
                                xlab="", ylab="Amount in 20 mL (mg/L)", main = "Mg accumulation in aeroponics vs soil") + theme(axis.text.x = element_text(angle = 90))
Mg_errorplot <- Mg_errorplot + stat_compare_means(method = "t.test", ref.group = "leaf", label = "p.signif")
Mg_errorplot

Mn_errorplot <- ggerrorplot(aero_ICPMS, y="Mn", x="Sample", fill="Sample",color = "Treatment",
                                desc_stat = "mean_sd", add="jitter", 
                                xlab="", ylab="Amount in 20 mL (mg/L)", main = "Mn accumulation in aeroponics vs soil") + theme(axis.text.x = element_text(angle = 90))
Mn_errorplot <- Mn_errorplot + stat_compare_means(method = "t.test", ref.group = "leaf", label = "p.signif")
Mn_errorplot

Mo_errorplot <- ggerrorplot(aero_ICPMS, y="Mo", x="Sample", fill="Sample", color = "Treatment",
                                desc_stat = "mean_sd", add="jitter",
                                xlab="", ylab="Amount in 20 mL (mg/L)", main = "Mo accumulation in aeroponics vs soil") + theme(axis.text.x = element_text(angle = 90))
Mo_errorplot <- Mo_errorplot + stat_compare_means(method = "t.test", ref.group = "leaf", label = "p.signif")
Mo_errorplot

Ni_errorplot <- ggerrorplot(aero_ICPMS, y="Ni", x="Sample", fill="Sample", color = "Treatment",
                                desc_stat = "mean_sd", add="jitter", 
                                xlab="", ylab="Amount in 20 mL (mg/L)", main = "Ni accumulation in aeroponics vs soil") + theme(axis.text.x = element_text(angle = 90))
Ni_errorplot <- Ni_errorplot + stat_compare_means(method = "t.test", ref.group = "leaf", label = "p.signif")
Ni_errorplot

P_errorplot <- ggerrorplot(aero_ICPMS, y="P", x="Sample", fill="Sample", color = "Treatment",
                                desc_stat = "mean_sd", add="jitter",
                                xlab="", ylab="Amount in 20 mL (mg/L)", main = "P accumulation in aeroponics vs soil") + theme(axis.text.x = element_text(angle = 90))
P_errorplot <- P_errorplot + stat_compare_means(method = "t.test", ref.group = "leaf", label = "p.signif")
P_errorplot

S_errorplot <- ggerrorplot(aero_ICPMS, y="S", x="Sample", fill="Sample", color = "Treatment",
                                desc_stat = "mean_sd", add="jitter",
                                xlab="", ylab="Amount in 20 mL (mg/L)", main = "S accumulation in aeroponics vs soil") + theme(axis.text.x = element_text(angle = 90))
S_errorplot <- S_errorplot + stat_compare_means(method = "t.test", ref.group = "leaf", label = "p.signif")
S_errorplot

Zn_errorplot <- ggerrorplot(aero_ICPMS, y="Zn", x="Sample", fill="Sample", color = "Treatment",
                                desc_stat = "mean_sd", add="jitter",
                                xlab="", ylab="Amount in 20 mL (mg/L)", main = "Zn accumulation in aeroponics vs soil") + theme(axis.text.x = element_text(angle = 90))
Zn_errorplot <- Zn_errorplot + stat_compare_means(method = "t.test", ref.group = "leaf", label = "p.signif")
Zn_errorplot

Na_errorplot <- ggerrorplot(aero_ICPMS, y="Na", x="Sample", fill="Sample", color = "Treatment",
                                desc_stat = "mean_sd", add="jitter",
                                xlab="", ylab="Amount in 20 mL (mg/L)", main = "Na accumulation in aeroponics vs soil") + theme(axis.text.x = element_text(angle = 90))
Na_errorplot <- Na_errorplot + stat_compare_means(method = "t.test", ref.group = "leaf", label = "p.signif")
Na_errorplot

Cu_errorplot <- ggerrorplot(aero_ICPMS, y="Cu", x="Sample", fill="Sample", color = "Treatment",
                                desc_stat = "mean_sd", add="jitter",
                                xlab="", ylab="Amount in 20 mL (mg/L)", main = "Cu accumulation in aeroponics vs soil") + theme(axis.text.x = element_text(angle = 90))
Cu_errorplot <- Cu_errorplot + stat_compare_means(method = "t.test", ref.group = "leaf", label = "p.signif")
Cu_errorplot

#conclusions
#shoot accumulation of Al, Fe, K, Mg, Mn, Mo, P, S, Zn, Na, and Cu are all not significantly different than leaf, but all are much more varied than the leaf samples
#shoot accumulation of B, Ca, and Ni are (*) significantly higher than leaf, but all are much more varied than the leaf samples