Amplificación de RT-qPCR
Samantha Carrillo
2026-03-17
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Instalación de paquetes pacman: llama otros paquetes y si no los instala
if(!require(pacman)) {
install.packages("pacman")
library(pacman)
}## Loading required package: pacman## Loading required package: pacmanLlamar pacman
library("pacman")Llamar paquetería necesaria
p_load("vroom",
"dplyr",
"ggplot2",
"tidyr")Llama base de datos
Curvas_amplif <- vroom(file = "https://raw.githubusercontent.com/ManuelLaraMVZ/resultados_PCR_practica/refs/heads/main/Ejemplo_amplificacion_RT-PCR.csv")## `curl` package not installed, falling back to using `url()`
## 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.modificar base de datos
Curvas_amplif2 <- Curvas_amplif %>%
mutate(Ciclos = Cycle, H20 = A1, JRWF = B1, PPOF = C1, MLL = D1, DDR = E1) %>% select(-Cycle:-E1) %>%
filter(Ciclos >=17)
Curvas_amplif2## # A tibble: 19 × 6
## Ciclos H20 JRWF PPOF MLL DDR
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 17 0.0000132 0.00126 -0.00121 0.000599 0.000786
## 2 18 0.0000394 0.000431 -0.000969 -0.00155 -0.00119
## 3 19 -0.000106 0.000227 -0.00145 -0.000874 -0.00113
## 4 20 -0.000104 0.000133 -0.00197 -0.000632 -0.00134
## 5 21 -0.000119 0.00104 0.000464 0.000245 -0.000417
## 6 22 -0.0000153 0.00028 0.0032 -0.00081 0.00158
## 7 23 0.0000704 -0.000086 0.00494 0.00162 0.000497
## 8 24 0.00012 -0.000238 0.0144 0.00139 0.00121
## 9 25 -0.0000899 -0.000484 0.0263 0.00634 0.00425
## 10 26 0.0000114 -0.00133 0.0491 0.0101 0.00894
## 11 27 -0.000104 -0.000824 0.0763 0.0202 0.0202
## 12 28 -0.000101 -0.000922 0.105 0.0365 0.0353
## 13 29 -0.000222 -0.000938 0.134 0.0624 0.0594
## 14 30 -0.0000675 -0.000187 0.162 0.0895 0.0823
## 15 31 -0.000089 -0.0000371 0.191 0.114 0.107
## 16 32 -0.000188 0.0018 0.220 0.141 0.128
## 17 33 -0.0000273 0.00345 0.243 0.170 0.152
## 18 34 0.000358 0.00615 0.268 0.197 0.173
## 19 35 0.000345 0.00913 0.293 0.223 0.192reordenar datos 1. seleccionar datos (variables dependientes) 2. agrupar variables por nombre 3. agrupar variables por sitio
Curvas_amplif3 <- Curvas_amplif2 %>%
pivot_longer(cols = -Ciclos,
names_to = "Muestras",
values_to = "Fluorescencias")
Curvas_amplif3## # A tibble: 95 × 3
## Ciclos Muestras Fluorescencias
## <dbl> <chr> <dbl>
## 1 17 H20 0.0000132
## 2 17 JRWF 0.00126
## 3 17 PPOF -0.00121
## 4 17 MLL 0.000599
## 5 17 DDR 0.000786
## 6 18 H20 0.0000394
## 7 18 JRWF 0.000431
## 8 18 PPOF -0.000969
## 9 18 MLL -0.00155
## 10 18 DDR -0.00119
## # ℹ 85 more rowsgraficar
Grafica_amplif <- ggplot(data = Curvas_amplif3,
mapping = aes(x = Ciclos,
y = Fluorescencias,
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 per session.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.Grafica_amplif 
Umbral_ciclos <- 0.008
Grafica_amplif2 <- Grafica_amplif +
geom_hline(yintercept = Umbral_ciclos, linetype = "dashed", color = "#F01A73")+
theme_classic()+
labs(title = "Cruvas de amplificación RT-qPCR",
subtitle = "Todas las muestras",
caption = "Diseñó:Ana Sofía Rodríguez ",
x= "Ciclos",
y = "Fluorescencias (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(breaks = seq(min(Curvas_amplif3$Fluorescencias),
max(Curvas_amplif3$Fluorescencias),
by = 0.02),
labels = scales:: number_format (accuracy = 0.02))## 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.Grafica_amplif2
Grafica_amplif_equipos <- ggplot(Curvas_amplif2,
aes(x = Ciclos,
y = MLL))+
geom_line(linewidth = 1.2, color = "#27F565" )+
geom_hline(yintercept = Umbral_ciclos, linetype = "dashed", color = "#F01A73")+
theme_classic()+
labs(title = "Cruvas de amplificación RT-qPCR",
subtitle = "Todas las muestras",
caption = "Diseñó:Ana Sofía Rodríguez ",
x= "Ciclos",
y = "Fluorescencias (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_amplif2$Ciclos),
max(Curvas_amplif2$Ciclos),
by = 2))+
scale_y_continuous(breaks = seq(min(Curvas_amplif2$MLL),
max(Curvas_amplif2$MLL),
by = 0.02),
labels = scales:: number_format (accuracy = 0.02))+
geom_line(aes(x = Ciclos,
y = H20),
color = "#279FF5",
linewidth = 1.5)
Grafica_amplif_equipos
Grafica_amplif_equipos <- ggplot(Curvas_amplif2,
aes(x = Ciclos))+
geom_line(aes(y = MLL, color = "MLL"),
linewidth = 1.2)+
geom_line(aes(y = H20, color = "H2O"),
linewidth = 1.5)+
geom_hline(yintercept = Umbral_ciclos,
linetype = "dashed",
color = "#F01A73")+
scale_color_manual(values = c("MLL" = "#27F565",
"H2O" = "#279FF5"))+
theme_classic()+
labs(title = "Curvas de amplificación RT-qPCR",
subtitle = "Todas las muestras",
caption = "Diseñó: Ana Sofía Rodríguez",
x = "Ciclos",
y = "Fluorescencias (u.a.)",
color = "Muestras")+
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_amplif2$Ciclos),
max(Curvas_amplif2$Ciclos),
by = 2))+
scale_y_continuous(breaks = seq(min(Curvas_amplif2$MLL),
max(Curvas_amplif2$MLL),
by = 0.02),
labels = scales::number_format(accuracy = 0.02))
Grafica_amplif_equipos