Curvas de amplificación RT-qPCR en R
Ian Atzin Gonzalez Islas
2026-03-17
Ejercicio R de PCR Los Chunks los obtengo con :Ctrl+Alt+I/Cmd+Opt+I, #ctrl shift m para el simbolo %>% Paquetería
if (!require(pacman)) install.packages("pacman", dependencies = T)## Cargando paquete requerido: pacmanlibrary(pacman)
p_load("vroom",
"dplyr",
"ggplot2",
"ggrepel",
"tidyr")Llamar base de datos
Curvas_amplif <- vroom(file = "https://raw.githubusercontent.com/ManuelLaraMVZ/resultados_PCR_practica/refs/heads/main/Ejemplo_amplificacion_RT-PCR.csv")## Rows: 35 Columns: 6
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## dbl (6): Cycle, A1, B1, C1, D1, E1
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Curvas_amplif## # A tibble: 35 × 6
## Cycle A1 B1 C1 D1 E1
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 1 0.0000213 -0.00531 0.0000279 0.000519 0.000468
## 2 2 -0.0000305 -0.00286 0.00179 0.000301 0.000462
## 3 3 -0.0000823 -0.00136 -0.000335 0.000842 0.0000266
## 4 4 -0.0000536 -0.00101 0.00166 0.000522 -0.000943
## 5 5 -0.0000565 -0.000787 0.000199 0.000586 0.0000877
## 6 6 0.000111 -0.000233 0.00231 0.000451 0.00076
## 7 7 0.000096 0.0000674 -0.000511 -0.00112 -0.000618
## 8 8 0.0000698 0.000602 -0.000595 -0.000944 0.00108
## 9 9 0.000202 0.00143 0.000166 0.000342 -0.000105
## 10 10 -0.00001 0.00101 -0.00136 -0.000254 0.00102
## # ℹ 25 more rowsCurvas_amplif2 <- Curvas_amplif %>%
mutate(Ciclos = Cycle, JFRW = A1, JRL = B1, PPOF = C1, MLL = D1, AALE = E1) %>%
select(-1:-6) %>%
filter(Ciclos >= 21)
Curvas_amplif2## # A tibble: 15 × 6
## Ciclos JFRW JRL PPOF MLL AALE
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 21 -0.000119 0.00104 0.000464 0.000245 -0.000417
## 2 22 -0.0000153 0.00028 0.0032 -0.00081 0.00158
## 3 23 0.0000704 -0.000086 0.00494 0.00162 0.000497
## 4 24 0.00012 -0.000238 0.0144 0.00139 0.00121
## 5 25 -0.0000899 -0.000484 0.0263 0.00634 0.00425
## 6 26 0.0000114 -0.00133 0.0491 0.0101 0.00894
## 7 27 -0.000104 -0.000824 0.0763 0.0202 0.0202
## 8 28 -0.000101 -0.000922 0.105 0.0365 0.0353
## 9 29 -0.000222 -0.000938 0.134 0.0624 0.0594
## 10 30 -0.0000675 -0.000187 0.162 0.0895 0.0823
## 11 31 -0.000089 -0.0000371 0.191 0.114 0.107
## 12 32 -0.000188 0.0018 0.220 0.141 0.128
## 13 33 -0.0000273 0.00345 0.243 0.170 0.152
## 14 34 0.000358 0.00615 0.268 0.197 0.173
## 15 35 0.000345 0.00913 0.293 0.223 0.192Curvas_amplif3 <- Curvas_amplif2 %>%
pivot_longer(cols = -Ciclos,
names_to = "Muestras",
values_to = "Fluorescencias")
Curvas_amplif3## # A tibble: 75 × 3
## Ciclos Muestras Fluorescencias
## <dbl> <chr> <dbl>
## 1 21 JFRW -0.000119
## 2 21 JRL 0.00104
## 3 21 PPOF 0.000464
## 4 21 MLL 0.000245
## 5 21 AALE -0.000417
## 6 22 JFRW -0.0000153
## 7 22 JRL 0.00028
## 8 22 PPOF 0.0032
## 9 22 MLL -0.00081
## 10 22 AALE 0.00158
## # ℹ 65 more rowsUmbral_ciclos <- 0.08
Curvas_amplif_grafica <- ggplot(Curvas_amplif3,
aes(x = Ciclos,
y = Fluorescencias,
color = Muestras)) +
geom_line(size = 1.5) +
geom_hline(yintercept = Umbral_ciclos, linetype = "dashed", color = "#581845") +
theme_classic() +
labs(title = "Curvas de amplificación RT-qPCR",
subtitle = "Práctica 1, \nEquipo: MLL",
caption = "Todas las muestras",
x = "Ciclos",
y = "Fluorescencia (u.a.)") +
theme(
axis.line = element_line(size = 1.2, 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))+
scale_y_continuous(labels = scales::number_format(accuracy = 0.05),
breaks = seq(min(Curvas_amplif3$Fluorescencias), max(Curvas_amplif3$Fluorescencias), by = 0.05))## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once per session.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.## 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 per session.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.Curvas_amplif_grafica
Grafica_equipos <- ggplot(Curvas_amplif2,
mapping = aes(x= Ciclos,
y = MLL))+
geom_line(color ="#6287f1", size = 1.5)+
geom_hline(yintercept = Umbral_ciclos, linetype = "dashed", color = "#581845") +
theme_classic() +
labs(title = "Curvas de amplificación RT-qPCR",
subtitle = "Muestra MLL",
caption = "Diseñó: Ian Atzin Gonzalez Islas",
x = "Ciclos",
y = "Fluorescencia (u.a.)") +
theme(
axis.line = element_line(size = 1.2, 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))+
scale_y_continuous(labels = scales::number_format(accuracy = 0.05),
breaks = seq(min(Curvas_amplif3$Fluorescencias), max(Curvas_amplif3$Fluorescencias), by = 0.05))
Grafica_equipos