Amplificación RT-qPCR
Julieta Tavera Tello
2026-03-16
#Cmd´+opt+I - Chunk
if(!require(pacman))
install.packages("pacman")## Loading required package: pacmanlibrary("pacman")Llamar paqueteria necesaria
install.packages("BiocManager") # Instala BiocManager## Installing package into '/cloud/lib/x86_64-pc-linux-gnu-library/4.5'
## (as 'lib' is unspecified)install.packages("ggplot2") # Instala ggplot2## Installing package into '/cloud/lib/x86_64-pc-linux-gnu-library/4.5'
## (as 'lib' is unspecified)library(BiocManager)
library(ggplot2)
# O con pacman:
pacman::p_load("vroom", "dplyr", "ggplot2", "tidyr")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.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 rowsModificar base de datos
Curvas_amplif2 <- Curvas_amplif %>%
mutate(Ciclos = Cycle, H2O = A1, JRWF = B1, PPOF = C1, JTT = D1, DDR = E1) %>% select(-Cycle:-E1)
Curvas_amplif2## # A tibble: 35 × 6
## Ciclos H2O JRWF PPOF JTT DDR
## <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 rowsReordenamiento de datos
- Seleccionar los datos a reordenar (variables dependientes)
- Agrupar por nombre
- Por ciclo
Curvas_amplif3 <- Curvas_amplif2 %>%
pivot_longer(cols = -Ciclos,
names_to = "Muestras",
values_to = "Fluoresencias")
Curvas_amplif3## # A tibble: 175 × 3
## Ciclos Muestras Fluoresencias
## <dbl> <chr> <dbl>
## 1 1 H2O 0.0000213
## 2 1 JRWF -0.00531
## 3 1 PPOF 0.0000279
## 4 1 JTT 0.000519
## 5 1 DDR 0.000468
## 6 2 H2O -0.0000305
## 7 2 JRWF -0.00286
## 8 2 PPOF 0.00179
## 9 2 JTT 0.000301
## 10 2 DDR 0.000462
## # ℹ 165 more rowsGráfica
Grafica_amplif <- ggplot(data = Curvas_amplif3, mapping = aes (x = Ciclos, y = Fluoresencias, color = Muestras)) +
geom_line (linewith = 1.5)## Warning in geom_line(linewith = 1.5): Ignoring unknown parameters: `linewith`Grafica_amplif
Mejorar la gráfica
Umbral_ciclos <- 0.008
Grafica_amplif <- Grafica_amplif+
geom_hline(yintercept = Umbral_ciclos, linetype = "dashed", color = "#A85994")+
theme_classic()+
labs(title = "Curvas de amplificación RT-qPCR",
subtitle = "Todas las muestras",
caption = "Diseño: Julieta Tavera",
x = "Ciclos",
y = "Fluoresencia (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$Fluoresencias),
max(Curvas_amplif3$Fluoresencias),
by = 0.02),
labels = scales:: number_format(accuracy = 0.05))## 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_amplif
Grafica_amplif_equipo <- ggplot(Curvas_amplif2, aes(x = Ciclos)) +
geom_line(aes(y = JTT, color = "JTT"), linewidth = 1.5) +
geom_line(aes(y = H2O, color = "H2O"), linewidth = 1.5) +
geom_hline(yintercept = Umbral_ciclos, linetype = "dashed", color = "#F54927") +
scale_color_manual(values = c("JTT" = "#EDB8AD", "H2O" = "#ADE9ED")) +
theme_classic() +
labs(title = "Curvas de amplificación RT-qPCR",
subtitle = "Todas las muestras",
caption = "Diseño: Julieta Tavera Tello",
x = "Ciclos",
y = "Fluorescencia (u.a.)",
color = "Muestras") +
theme(axis.line = element_line(linewidth = 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$JTT),
max(Curvas_amplif2$JTT),
by = 0.02),
labels = scales::number_format(accuracy = 0.02))
Grafica_amplif_equipo