Amplificacion RTqPCR
Equipo 1
2025-03-26
Instalación de paquetes Pacman
if(!require(pacman))
install.packages("pacman")## Loading required package: pacmanlibrary("pacman")Llamar paqueteria necesaria
p_load("vroom",
"dplyr",
"ggplot2",
"tidyr" )Llamar a base de datos
Curvas_amplif <- read.csv(file="https://raw.githubusercontent.com/ManuelLaraMVZ/resultados_PCR_practica/refs/heads/main/Amplif_grupo2_17022025.csv")
Curvas_amplif## Cycle A1 B1 C1 D1 E1
## 1 1 -130.5302484 -27.420108 -23.4846130 -60.7470105 -20.0380601
## 2 2 -48.6828056 1.200377 -3.2706757 -15.0623155 1.7599193
## 3 3 -26.4325027 10.314809 0.8156109 -6.8512508 6.5105286
## 4 4 -11.1609463 11.923687 2.6658889 6.8659362 6.9622847
## 5 5 -5.5519322 13.099167 0.9680155 7.7414393 5.7836178
## 6 6 -3.1364494 12.631298 4.0684877 -0.5178159 1.0165572
## 7 7 -0.6675344 14.306466 6.7213583 3.7621350 5.3595559
## 8 8 -4.1413492 17.781415 3.8933444 -0.2126059 0.7374334
## 9 9 -6.7724948 14.000995 -5.4027631 1.8723613 -0.6639075
## 10 10 -0.1776662 16.109365 0.1029792 -1.3790445 -4.5110047
## 11 11 3.9860396 17.139972 0.1133305 5.7271861 0.1864360
## 12 12 -3.1288300 12.387640 4.3835122 1.0031560 -3.0809283
## 13 13 -1.5798798 11.696081 0.3990870 -1.9592870 -7.1114996
## 14 14 1.7684743 8.756399 4.9446811 1.7029845 -3.8336917
## 15 15 -1.0480298 20.697060 6.8481278 2.6972633 -1.4239648
## 16 16 -0.9978187 17.219311 25.4974932 3.7173948 -1.6814489
## 17 17 3.0478430 33.891979 44.9621920 15.4768549 -6.3953409
## 18 18 -1.8983324 49.591515 82.2117926 31.1271357 -6.7847709
## 19 19 -4.9114141 84.614673 151.4289012 56.1489946 -7.3590715
## 20 20 -6.3738257 118.125207 241.2039719 92.5943013 -4.6466738
## 21 21 -8.7552252 172.364916 412.6108338 174.4002413 -5.3907238
## 22 22 -4.1051973 232.466343 623.3814133 265.3550855 -7.5022804
## 23 23 2.2403730 301.187182 885.8754648 390.5962003 -7.0895472
## 24 24 -2.4026281 371.967290 1180.0350090 525.7784668 -7.9263438
## 25 25 -1.7353687 447.794678 1483.3341950 675.4369892 -1.2438599
## 26 26 2.7039360 519.087125 1770.9125280 831.3390109 4.2028195
## 27 27 7.3410221 589.924228 2030.7907600 993.8488203 -0.5241759
## 28 28 31.1168906 655.687297 2254.2891930 1149.1336250 7.6437916
## 29 29 60.5305504 710.956722 2432.6846390 1292.4698800 11.5259657
## 30 30 101.5649836 754.255479 2572.5314340 1416.4660060 13.9227662
## 31 31 147.5153188 788.721504 2674.2767600 1522.4804940 32.0145518
## 32 32 198.3025345 817.202239 2747.8749140 1611.5912660 40.0374699
## 33 33 262.0854221 835.811427 2797.4411300 1682.4396090 74.8234689
## 34 34 332.4228470 848.615480 2829.3361800 1737.1993240 115.4316139
## 35 35 406.9492803 853.519593 2850.5403220 1772.2678560 191.2276918
## 36 36 488.1221868 860.075579 2861.8114120 1793.5527760 294.7195498
## 37 37 572.4151303 857.451767 2869.0124190 1805.1803550 456.9145421
## 38 38 658.3116161 856.090208 2871.3460450 1814.9116200 640.1365760
## 39 39 743.0515640 849.763968 2872.6102820 1821.7464150 846.7123183
## 40 40 825.0751987 843.731051 2871.8544380 1827.3238630 1061.2097820
## H1
## 1 -104.6974289
## 2 -30.4569498
## 3 2.0749456
## 4 19.1494076
## 5 18.9645566
## 6 13.6925910
## 7 10.1573977
## 8 4.1100851
## 9 4.0301079
## 10 5.0949633
## 11 8.9592194
## 12 -5.2236110
## 13 -0.6503485
## 14 -4.0163025
## 15 -7.3288339
## 16 -5.8961883
## 17 -2.4660613
## 18 -4.2284104
## 19 -9.5379355
## 20 -13.1143588
## 21 -10.6041951
## 22 -12.7338467
## 23 -11.1694991
## 24 -22.4219517
## 25 -15.6529331
## 26 -22.0029051
## 27 -24.3298720
## 28 -22.5555271
## 29 -18.0203277
## 30 -31.5075760
## 31 -26.3033732
## 32 -24.2663614
## 33 -24.6468144
## 34 -15.7488516
## 35 -5.6414291
## 36 -1.9354642
## 37 11.5635303
## 38 36.0259909
## 39 53.5728802
## 40 73.4477193Modificar base de datos
Curvas_amplif2 <- Curvas_amplif %>%
mutate(Ciclos=Cycle, Manuel=A1, Regina=B1, Marian=C1, Ricardo=D1, Neto=E1, Johan=H1) %>%
select(-Cycle:-E1) %>%
filter(Ciclos>= 15)
Curvas_amplif2## H1 Ciclos Manuel Regina Marian Ricardo Neto
## 1 -7.328834 15 -1.0480298 20.69706 6.848128 2.697263 -1.4239648
## 2 -5.896188 16 -0.9978187 17.21931 25.497493 3.717395 -1.6814489
## 3 -2.466061 17 3.0478430 33.89198 44.962192 15.476855 -6.3953409
## 4 -4.228410 18 -1.8983324 49.59152 82.211793 31.127136 -6.7847709
## 5 -9.537935 19 -4.9114141 84.61467 151.428901 56.148995 -7.3590715
## 6 -13.114359 20 -6.3738257 118.12521 241.203972 92.594301 -4.6466738
## 7 -10.604195 21 -8.7552252 172.36492 412.610834 174.400241 -5.3907238
## 8 -12.733847 22 -4.1051973 232.46634 623.381413 265.355085 -7.5022804
## 9 -11.169499 23 2.2403730 301.18718 885.875465 390.596200 -7.0895472
## 10 -22.421952 24 -2.4026281 371.96729 1180.035009 525.778467 -7.9263438
## 11 -15.652933 25 -1.7353687 447.79468 1483.334195 675.436989 -1.2438599
## 12 -22.002905 26 2.7039360 519.08713 1770.912528 831.339011 4.2028195
## 13 -24.329872 27 7.3410221 589.92423 2030.790760 993.848820 -0.5241759
## 14 -22.555527 28 31.1168906 655.68730 2254.289193 1149.133625 7.6437916
## 15 -18.020328 29 60.5305504 710.95672 2432.684639 1292.469880 11.5259657
## 16 -31.507576 30 101.5649836 754.25548 2572.531434 1416.466006 13.9227662
## 17 -26.303373 31 147.5153188 788.72150 2674.276760 1522.480494 32.0145518
## 18 -24.266361 32 198.3025345 817.20224 2747.874914 1611.591266 40.0374699
## 19 -24.646814 33 262.0854221 835.81143 2797.441130 1682.439609 74.8234689
## 20 -15.748852 34 332.4228470 848.61548 2829.336180 1737.199324 115.4316139
## 21 -5.641429 35 406.9492803 853.51959 2850.540322 1772.267856 191.2276918
## 22 -1.935464 36 488.1221868 860.07558 2861.811412 1793.552776 294.7195498
## 23 11.563530 37 572.4151303 857.45177 2869.012419 1805.180355 456.9145421
## 24 36.025991 38 658.3116161 856.09021 2871.346045 1814.911620 640.1365760
## 25 53.572880 39 743.0515640 849.76397 2872.610282 1821.746415 846.7123183
## 26 73.447719 40 825.0751987 843.73105 2871.854438 1827.323863 1061.2097820
## Johan
## 1 -7.328834
## 2 -5.896188
## 3 -2.466061
## 4 -4.228410
## 5 -9.537935
## 6 -13.114359
## 7 -10.604195
## 8 -12.733847
## 9 -11.169499
## 10 -22.421952
## 11 -15.652933
## 12 -22.002905
## 13 -24.329872
## 14 -22.555527
## 15 -18.020328
## 16 -31.507576
## 17 -26.303373
## 18 -24.266361
## 19 -24.646814
## 20 -15.748852
## 21 -5.641429
## 22 -1.935464
## 23 11.563530
## 24 36.025991
## 25 53.572880
## 26 73.447719Reordenamiento de datos 1. Seleccionar los datos a reordenar (variables dependientes) 2. Agrupare todas las variables por nombre 3. Agrupare todas las variables por ciclo
Curvas_amplif3 <- Curvas_amplif2 %>%
pivot_longer(cols = -Ciclos,
names_to = "Muestras",
values_to = "Fluorescencia")
Curvas_amplif3## # A tibble: 182 × 3
## Ciclos Muestras Fluorescencia
## <int> <chr> <dbl>
## 1 15 H1 -7.33
## 2 15 Manuel -1.05
## 3 15 Regina 20.7
## 4 15 Marian 6.85
## 5 15 Ricardo 2.70
## 6 15 Neto -1.42
## 7 15 Johan -7.33
## 8 16 H1 -5.90
## 9 16 Manuel -0.998
## 10 16 Regina 17.2
## # ℹ 172 more rowsGrafica
Grafica_amplif <- ggplot(data = Curvas_amplif3,
mapping = aes(x=Ciclos,
y=Fluorescencia,
color=Muestras)) +
geom_line(size=1.5)## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.Grafica_amplif
Mejorar la grafica
Umbral_ciclos <- 100
Grafica_amplif2 <- Grafica_amplif +
geom_hline(yintercept = Umbral_ciclos, linetype="dashed", color="red")+
theme_classic()+
labs(title = "Curvas de amplificación RT-qPCR",
subtitle = "Todas las muestras",
caption = "Diseño:Equipo 1",
x="Ciclos",
y="Fluorescencia (u.a.)")+
theme(axis.line = element_line(size=1, color="black"),
axis.title = element_text(face = "bold"),
axis.text = element_text(face = "bold"),
legend.title = element_text(face = "bold"),
legend.text = element_text(face = "bold"))+
scale_x_continuous(breaks = seq(min(Curvas_amplif3$Ciclos),
max(Curvas_amplif3$Ciclos),
by=2))## Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
## ℹ Please use the `linewidth` argument instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.Grafica_amplif2
Grafica de los datos del equipo
Grafica_amplif_equipo <- ggplot(Curvas_amplif2,
aes(x=Ciclos,
y=Regina))+
geom_line(linewidth=1.2, color="pink")+
geom_hline(yintercept = Umbral_ciclos, linetype="dashed", color="red")+
theme_classic()+
labs(title = "Curvas de amplificación RT-qPCR",
subtitle = "Todas las muestras",
caption = "Diseño:Equipo 1",
x="Ciclos",
y="Fluorescencia (u.a.)")+
theme(axis.line = element_line(size=1, color="black"),
axis.title = element_text(face = "bold"),
axis.text = element_text(face = "bold"),
legend.title = element_text(face = "bold"),
legend.text = element_text(face = "bold"))+
scale_x_continuous(breaks = seq(min(Curvas_amplif3$Ciclos),
max(Curvas_amplif3$Ciclos),
by=2))+
geom_line(aes(x=Ciclos,
y=Manuel),
color="blue",
linewidth=1.2)
Grafica_amplif_equipo
library(ggplot2)
library(tidyr)
# Transformar los datos al formato largo
Curvas_amplif_long <- Curvas_amplif2 %>%
pivot_longer(cols = c(Regina, Manuel),
names_to = "Muestra",
values_to = "Fluorescencia")
Umbral_ciclos <- 100
Grafica_amplif_equipo <- ggplot(Curvas_amplif_long, aes(x = Ciclos, y = Fluorescencia, color = Muestra)) +
geom_line(linewidth = 1.2) +
geom_hline(yintercept = Umbral_ciclos, linetype = "dashed", color = "red") +
theme_classic() +
labs(title = "Curvas de amplificación RT-qPCR",
subtitle = "Todas las muestras",
caption = "Diseño: Equipo 1",
x = "Ciclos",
y = "Fluorescencia (u.a.)") +
theme(axis.line = element_line(size = 1, color = "black"),
axis.title = element_text(face = "bold"),
axis.text = element_text(face = "bold"),
legend.title = element_text(face = "bold"),
legend.text = element_text(face = "bold")) +
scale_x_continuous(breaks = seq(min(Curvas_amplif2$Ciclos),
max(Curvas_amplif2$Ciclos),
by = 2)) +
scale_color_manual(values = c("Regina" = "pink", "Manuel" = "blue"))
print(Grafica_amplif_equipo)