Curva de amplificación valores absolutos
Paulina Aguilar
2026-05-01
if (!require(pacman))
install.packages("pacman")## Loading required package: pacmanLlamar a pacman
library("pacman")Llamar paqueteria necesaria
p_load("vroom",
"dplyr",
"ggplot2",
"tidyr")Llamar a base de datos
Curvas_amplif <- vroom(file ="https://raw.githubusercontent.com/ManuelLaraMVZ/Metabolomica_2026_1/refs/heads/main/Amplificacion_ambos%20grupos.csv")## Rows: 51 Columns: 9
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## dbl (9): Cycle, 50 ng, 10 ng, 5 ng, 1 ng, 0.5 ng, 0.1 ng, G1-M, G2-M
##
## 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: 51 × 9
## Cycle `50 ng` `10 ng` `5 ng` `1 ng` `0.5 ng` `0.1 ng` `G1-M` `G2-M`
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 1 21.3 0.124 -2.25 2.06 -1.78 -2.32 22.1 -0.184
## 2 2 27.9 1.39 2.61 8.66 5.96 2.18 92.0 8.29
## 3 3 34.5 -0.660 11.4 12.2 5.94 2.34 132. 3.73
## 4 4 56.6 1.000 1.87 6.49 5.20 1.05 164. 3.20
## 5 5 65.2 -0.484 -1.18 1.77 -5.23 0.606 184. 0.557
## 6 6 72.3 1.44 -0.477 2.35 -0.958 4.81 214. 0.0300
## 7 7 89.1 -5.10 -3.87 -4.93 -3.60 -4.87 249. -7.37
## 8 8 101. -1.67 -3.52 -3.31 -2.34 0.403 277. -6.98
## 9 9 114. 2.66 5.35 -2.11 -1.40 -0.659 302. -3.63
## 10 10 123. 13.6 10.4 -5.98 2.27 1.13 332. -1.16
## # ℹ 41 more rowsModificar base de datos
Curvas_amplif2 <- Curvas_amplif %>%
rename(
Ciclos = Cycle,
JPP = `G2-M`) %>%
select(-"50 ng":-"10 ng")
#filter(Ciclos >= 10)
Curvas_amplif2## # A tibble: 51 × 7
## Ciclos `5 ng` `1 ng` `0.5 ng` `0.1 ng` `G1-M` JPP
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 1 -2.25 2.06 -1.78 -2.32 22.1 -0.184
## 2 2 2.61 8.66 5.96 2.18 92.0 8.29
## 3 3 11.4 12.2 5.94 2.34 132. 3.73
## 4 4 1.87 6.49 5.20 1.05 164. 3.20
## 5 5 -1.18 1.77 -5.23 0.606 184. 0.557
## 6 6 -0.477 2.35 -0.958 4.81 214. 0.0300
## 7 7 -3.87 -4.93 -3.60 -4.87 249. -7.37
## 8 8 -3.52 -3.31 -2.34 0.403 277. -6.98
## 9 9 5.35 -2.11 -1.40 -0.659 302. -3.63
## 10 10 10.4 -5.98 2.27 1.13 332. -1.16
## # ℹ 41 more rowsReordenamiento de datos
- Seleccionar los datos a reordenar (variables dependientes)
- Agrupar todas las variables por nombre
- Agrupar todas las variables por ciclo.
Curvas_amplif3 <- Curvas_amplif2 %>%
pivot_longer(cols= -Ciclos,
names_to = "Muestras",
values_to = "Fluorescencias")
Curvas_amplif3## # A tibble: 306 × 3
## Ciclos Muestras Fluorescencias
## <dbl> <chr> <dbl>
## 1 1 5 ng -2.25
## 2 1 1 ng 2.06
## 3 1 0.5 ng -1.78
## 4 1 0.1 ng -2.32
## 5 1 G1-M 22.1
## 6 1 JPP -0.184
## 7 2 5 ng 2.61
## 8 2 1 ng 8.66
## 9 2 0.5 ng 5.96
## 10 2 0.1 ng 2.18
## # ℹ 296 more rowsGrafica
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
Mejorar la gráfica
Umbral_ciclos <- 0.1
Grafica_amplif2 <- Grafica_amplif+
geom_hline(yintercept=Umbral_ciclos, linetype="dashed", color="#91197C")+
theme_classic()+
labs(title="Curvas de amplificación de valores absolutos RT-qPCR",
subtitle="Todas las muestras",
caption="Equipo: JPP",
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=5))+
scale_y_continuous(breaks = seq(min(Curvas_amplif3$Fluorescencias),
max(Curvas_amplif3$Fluorescencias),
by=80),
labels = scales::number_format(accuracy = 1))## 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 de los datos del equipo
Grafica_amplif_equipo <- ggplot(Curvas_amplif2, aes(x = Ciclos)) +
geom_line(aes(y = JPP, color = "JPP"), linewidth = 1.5) +
geom_hline(yintercept = Umbral_ciclos,
linetype = "dashed",
color = "#91197C",
linewidth = 1) +
scale_color_manual(
name = "Muestras",
values = c("JPP" = "#6AA84F",
"MLL" = "#2E2A8C")
) +
theme_classic() +
labs(
title = "Curvas de amplificación de valores absolutos RT-qPCR",
subtitle = "EQUIPO JPP",
caption = "Equipo: JPP",
x = "Ciclos",
y = "Fluorescencia (u.a.)"
) +
theme(
axis.line = element_line(linewidth = 1.2, color = "black"),
axis.title = element_text(face = "bold", size = 12),
axis.text = element_text(face = "bold", size = 10),
legend.title = element_text(face = "bold", size = 12),
legend.text = element_text(face = "bold", size = 10),
plot.title = element_text(face = "bold", size = 14),
plot.subtitle = element_text(size = 12)
) +
scale_x_continuous(
breaks = seq(min(Curvas_amplif2$Ciclos),
max(Curvas_amplif2$Ciclos),
by = 3)
) +
scale_y_continuous(
breaks = seq(0, max(Curvas_amplif2$JPP), by = 40),
labels = scales::number_format(accuracy = 1)
)
Grafica_amplif_equipo