Experimento - 1 efecto de seca em microton transgénico genes PR
library(agricolae)
library(readxl)
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library(tmap)
library(rgdal)
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library(ggplot2)
library(gridExtra)
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library(readxl)
## Experimento de seca 1
# potes pequeños
exp <- read_excel("C:/Users/User/Desktop/exp.xlsx",
sheet = "expe1")
attach(exp)
head(exp)
## # A tibble: 6 x 9
## genot Planta cc Rept numfo areafol folhas talo raiz
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 VF 1 100 3 15 123. 0.5 0.55 0.17
## 2 MT 2 30 3 11 95.2 0.28 0.36 0.14
## 3 MT 3 100 2 11 112. 0.46 0.36 0.15
## 4 VG 4 100 1 12 124. 0.5 0.36 0.21
## 5 VG 5 60 2 9 62.4 0.26 0.2 0.13
## 6 VØ 6 30 4 7 53.2 0.23 0.2 0.08
a <- as.factor(genot)
b <- as.factor(cc)
inter<-as.factor(a:b)
############ 1.1 anova Numero de folhas ###########################
summary(aov(numfo ~ a+b+inter, data = exp))
## Df Sum Sq Mean Sq F value Pr(>F)
## a 3 56.72 18.906 4.900 0.00474 **
## b 2 29.10 14.550 3.771 0.03012 *
## inter 6 17.83 2.972 0.770 0.59699
## Residuals 48 185.20 3.858
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
LSD.test(aov(numfo ~ a + b + inter, data = exp),
"a", alpha = 0.05)["groups"]
## $groups
## numfo groups
## VF 12.46667 a
## VØ 11.13333 ab
## VG 10.13333 b
## MT 10.06667 b
LSD.test(aov(numfo ~ a + b + inter, data = exp),
"b", alpha = 0.05)["groups"]
## $groups
## numfo groups
## 100 11.65 a
## 60 11.20 ab
## 30 10.00 b
LSD.test(aov(numfo ~ a + b + inter, data = exp),
"inter", alpha = 0.05)["groups"]
## $groups
## numfo groups
## VF:100 13.2 a
## VF:60 12.8 ab
## VØ:60 12.4 abc
## VØ:100 11.6 abcd
## VF:30 11.4 abcd
## VG:100 11.4 abcd
## MT:100 10.4 bcd
## MT:60 10.2 cd
## MT:30 9.6 d
## VG:30 9.6 d
## VG:60 9.4 d
## VØ:30 9.4 d
shapiro.test(unlist(aov(numfo ~ a + b + inter,
data = exp)["residuals"]))
##
## Shapiro-Wilk normality test
##
## data: unlist(aov(numfo ~ a + b + inter, data = exp)["residuals"])
## W = 0.97567, p-value = 0.2735
res <-sort(unlist(aov( numfo ~ a + b + inter,
data = exp)["residuals"]),decreasing = TRUE)
ks.test(res, "pnorm" ,mean(res),sd(res))
## Warning in ks.test(res, "pnorm", mean(res), sd(res)): ties should not be present
## for the Kolmogorov-Smirnov test
##
## One-sample Kolmogorov-Smirnov test
##
## data: res
## D = 0.1159, p-value = 0.3959
## alternative hypothesis: two-sided
kruskal(numfo, inter)["groups"]
## $groups
## numfo groups
## VF:100 47.3 a
## VF:60 44.4 ab
## VØ:60 42.3 ab
## VØ:100 34.6 abc
## VG:100 34.4 abc
## VF:30 34.3 abc
## MT:100 27.0 bc
## MT:60 24.9 bc
## MT:30 19.8 c
## VG:30 19.6 c
## VØ:30 19.4 c
## VG:60 18.0 c
############ 1.1 anova area foliar ###########################
summary(aov(areafol ~ a+b+inter, data = exp))
## Df Sum Sq Mean Sq F value Pr(>F)
## a 3 1162 387.4 0.831 0.48326
## b 2 6000 3000.1 6.437 0.00334 **
## inter 6 4287 714.5 1.533 0.18775
## Residuals 48 22370 466.0
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
LSD.test(aov(areafol ~ a + b + inter, data = exp),
"a", alpha = 0.05)["groups"]
## $groups
## areafol groups
## MT 91.24133 a
## VF 88.07067 a
## VG 82.65933 a
## VØ 80.03733 a
LSD.test(aov(areafol ~ a + b + inter, data = exp),
"b", alpha = 0.05)["groups"]
## $groups
## areafol groups
## 100 99.2535 a
## 60 81.4865 b
## 30 75.7665 b
LSD.test(aov(areafol ~ a + b + inter, data = exp),
"inter", alpha = 0.05)["groups"]
## $groups
## areafol groups
## VF:100 106.674 a
## VG:100 106.660 a
## MT:100 102.400 ab
## VØ:60 90.522 abc
## MT:60 87.148 abcd
## VF:60 85.820 abcd
## MT:30 84.176 abcd
## VØ:100 81.280 abcd
## VG:30 78.862 bcd
## VF:30 71.718 cd
## VØ:30 68.310 cd
## VG:60 62.456 d
shapiro.test(unlist(aov(areafol ~ a + b + inter,
data = exp)["residuals"]))
##
## Shapiro-Wilk normality test
##
## data: unlist(aov(areafol ~ a + b + inter, data = exp)["residuals"])
## W = 0.9707, p-value = 0.1578
res <-sort(unlist(aov( areafol ~ a + b + inter,
data = exp)["residuals"]),decreasing = TRUE)
ks.test(res, "pnorm" ,mean(res),sd(res))
##
## One-sample Kolmogorov-Smirnov test
##
## data: res
## D = 0.12063, p-value = 0.3208
## alternative hypothesis: two-sided
kruskal(areafol, inter)["groups"]
## $groups
## areafol groups
## VF:100 44.4 a
## VG:100 44.2 a
## MT:100 42.4 ab
## VØ:60 34.2 abc
## MT:60 32.8 abc
## MT:30 31.2 abc
## VF:60 29.2 abc
## VØ:100 27.4 abc
## VG:30 25.2 abc
## VF:30 22.5 bc
## VG:60 17.1 c
## VØ:30 15.4 c
############ 1.1 anova Biomassa de folhas ###########################
summary(aov(folhas ~ a+b+inter, data = exp))
## Df Sum Sq Mean Sq F value Pr(>F)
## a 3 0.0143 0.00476 0.613 0.609920
## b 2 0.1646 0.08232 10.602 0.000158 ***
## inter 6 0.0225 0.00374 0.482 0.818357
## Residuals 47 0.3649 0.00776
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 1 observation deleted due to missingness
LSD.test(aov(folhas ~ a + b + inter, data = exp),
"a", alpha = 0.05)["groups"]
## $groups
## folhas groups
## VG 0.3435714 a
## MT 0.3293333 a
## VØ 0.3140000 a
## VF 0.3020000 a
LSD.test(aov(folhas ~ a + b + inter, data = exp),
"b", alpha = 0.05)["groups"]
## $groups
## folhas groups
## 100 0.3900 a
## 60 0.3175 b
## 30 0.2615 b
LSD.test(aov(folhas ~ a + b + inter, data = exp),
"inter", alpha = 0.05)["groups"]
## $groups
## folhas groups
## VG:100 0.430 a
## MT:100 0.398 ab
## VF:100 0.386 abc
## VØ:100 0.354 abcd
## VØ:60 0.352 abcd
## MT:60 0.322 abcde
## VG:60 0.318 abcde
## VG:30 0.300 bcde
## VF:60 0.278 cde
## MT:30 0.268 de
## VF:30 0.242 de
## VØ:30 0.236 e
shapiro.test(unlist(aov(folhas ~ a + b + inter,
data = exp)["residuals"]))
##
## Shapiro-Wilk normality test
##
## data: unlist(aov(folhas ~ a + b + inter, data = exp)["residuals"])
## W = 0.98597, p-value = 0.7298
res <-sort(unlist(aov( folhas ~ a + b + inter,
data = exp)["residuals"]),decreasing = TRUE)
ks.test(res, "pnorm" ,mean(res),sd(res))
## Warning in ks.test(res, "pnorm", mean(res), sd(res)): ties should not be present
## for the Kolmogorov-Smirnov test
##
## One-sample Kolmogorov-Smirnov test
##
## data: res
## D = 0.07276, p-value = 0.9136
## alternative hypothesis: two-sided
kruskal(folhas, inter)["groups"]
## $groups
## folhas groups
## VG:100 47.5 a
## MT:100 42.6 ab
## VF:100 41.1 abc
## VØ:100 35.4 abcd
## VØ:60 34.7 abcd
## MT:60 34.0 abcd
## VG:60 27.1 abcde
## VG:30 26.7 bcde
## MT:30 21.6 cde
## VF:60 21.6 cde
## VF:30 17.4 de
## VØ:30 13.8 e
############ 1.1 anova Biomassa de talo ###########################
summary(aov(talo ~ a+b+inter, data = exp))
## Df Sum Sq Mean Sq F value Pr(>F)
## a 3 0.0229 0.00762 1.128 0.347
## b 2 0.1729 0.08647 12.803 3.64e-05 ***
## inter 6 0.0308 0.00514 0.761 0.604
## Residuals 47 0.3174 0.00675
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 1 observation deleted due to missingness
LSD.test(aov(talo ~ a + b + inter, data = exp),
"a", alpha = 0.05)["groups"]
## $groups
## talo groups
## MT 0.3360000 a
## VF 0.3313333 a
## VG 0.2986667 a
## VØ 0.2907143 a
LSD.test(aov(talo ~ a + b + inter, data = exp),
"b", alpha = 0.05)["groups"]
## $groups
## talo groups
## 100 0.3795000 a
## 60 0.3163158 b
## 30 0.2480000 c
LSD.test(aov(talo ~ a + b + inter, data = exp),
"inter", alpha = 0.05)["groups"]
## $groups
## talo groups
## MT:100 0.4240 a
## VF:100 0.4200 a
## VØ:100 0.3420 ab
## VØ:60 0.3375 ab
## VG:100 0.3320 ab
## MT:60 0.3200 ab
## VF:60 0.3100 b
## VG:60 0.3020 bc
## MT:30 0.2640 bc
## VF:30 0.2640 bc
## VG:30 0.2620 bc
## VØ:30 0.2020 c
shapiro.test(unlist(aov(talo ~ a + b + inter,
data = exp)["residuals"]))
##
## Shapiro-Wilk normality test
##
## data: unlist(aov(talo ~ a + b + inter, data = exp)["residuals"])
## W = 0.97841, p-value = 0.3762
res <-sort(unlist(aov( talo ~ a + b + inter,
data = exp)["residuals"]),decreasing = TRUE)
ks.test(res, "pnorm" ,mean(res),sd(res))
## Warning in ks.test(res, "pnorm", mean(res), sd(res)): ties should not be present
## for the Kolmogorov-Smirnov test
##
## One-sample Kolmogorov-Smirnov test
##
## data: res
## D = 0.080472, p-value = 0.8394
## alternative hypothesis: two-sided
kruskal(talo, inter)["groups"]
## $groups
## talo groups
## MT:100 50.300 a
## VF:100 47.700 a
## VG:100 35.000 ab
## VØ:60 34.125 ab
## MT:60 32.900 ab
## VØ:100 32.600 ab
## VF:60 29.600 b
## VG:60 27.800 b
## VF:30 21.600 bc
## MT:30 20.800 bc
## VG:30 20.700 bc
## VØ:30 7.700 c
############ 1.1 anova Biomassa de raiz ###########################
summary(aov(raiz ~ a+b+inter, data = exp))
## Df Sum Sq Mean Sq F value Pr(>F)
## a 3 0.00019 0.0000627 0.033 0.992
## b 2 0.00086 0.0004314 0.228 0.797
## inter 6 0.00856 0.0014267 0.753 0.610
## Residuals 47 0.08904 0.0018945
## 1 observation deleted due to missingness
LSD.test(aov(raiz ~ a + b + inter, data = exp),
"a", alpha = 0.05)["groups"]
## $groups
## raiz groups
## MT 0.1253333 a
## VG 0.1242857 a
## VF 0.1213333 a
## VØ 0.1213333 a
LSD.test(aov(raiz ~ a + b + inter, data = exp),
"b", alpha = 0.05)["groups"]
## $groups
## raiz groups
## 100 0.1284211 a
## 60 0.1215000 a
## 30 0.1195000 a
LSD.test(aov(raiz ~ a + b + inter, data = exp),
"inter", alpha = 0.05)["groups"]
## $groups
## raiz groups
## VØ:60 0.144 a
## VF:100 0.140 a
## MT:100 0.134 a
## VG:100 0.130 a
## VF:30 0.126 a
## VG:60 0.126 a
## MT:30 0.124 a
## VG:30 0.118 a
## MT:60 0.118 a
## VØ:100 0.110 a
## VØ:30 0.110 a
## VF:60 0.098 a
shapiro.test(unlist(aov(raiz ~ a + b + inter,
data = exp)["residuals"]))
##
## Shapiro-Wilk normality test
##
## data: unlist(aov(raiz ~ a + b + inter, data = exp)["residuals"])
## W = 0.98833, p-value = 0.8435
res <-sort(unlist(aov( raiz ~ a + b + inter,
data = exp)["residuals"]),decreasing = TRUE)
ks.test(res, "pnorm" ,mean(res),sd(res))
## Warning in ks.test(res, "pnorm", mean(res), sd(res)): ties should not be present
## for the Kolmogorov-Smirnov test
##
## One-sample Kolmogorov-Smirnov test
##
## data: res
## D = 0.084614, p-value = 0.7921
## alternative hypothesis: two-sided
kruskal(raiz, inter)["groups"]
## $groups
## raiz groups
## VF:100 38.4 a
## VØ:60 37.8 a
## MT:100 35.3 a
## VF:30 34.5 a
## VG:60 31.7 a
## MT:30 31.1 a
## VG:100 30.0 a
## MT:60 28.5 a
## VG:30 28.1 a
## VØ:30 24.0 a
## VØ:100 21.5 a
## VF:60 19.1 a