Amplificación RT-qPCR
Campos-Hernández-Palos
2025-03-27
Instalación de paquetes
if(!require(pacman))
install.packages("pacman")## Loading required package: pacmanLlamar a pacman
library("pacman")Llamar paquetería necesaria
p_load("vroom",
"dplyr",
"ggplot2",
"tidyr")Llamar a base de datos
Curvas_amplif <- vroom (file = "https://raw.githubusercontent.com/ManuelLaraMVZ/resultados_PCR_practica/refs/heads/main/Amplif_grupo2_17022025.csv")## `curl` package not installed, falling back to using `url()`
## Rows: 40 Columns: 7
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## dbl (7): Cycle, A1, B1, C1, D1, E1, H1
##
## 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: 40 × 7
## Cycle A1 B1 C1 D1 E1 H1
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 1 -131. -27.4 -23.5 -60.7 -20.0 -105.
## 2 2 -48.7 1.20 -3.27 -15.1 1.76 -30.5
## 3 3 -26.4 10.3 0.816 -6.85 6.51 2.07
## 4 4 -11.2 11.9 2.67 6.87 6.96 19.1
## 5 5 -5.55 13.1 0.968 7.74 5.78 19.0
## 6 6 -3.14 12.6 4.07 -0.518 1.02 13.7
## 7 7 -0.668 14.3 6.72 3.76 5.36 10.2
## 8 8 -4.14 17.8 3.89 -0.213 0.737 4.11
## 9 9 -6.77 14.0 -5.40 1.87 -0.664 4.03
## 10 10 -0.178 16.1 0.103 -1.38 -4.51 5.09
## # ℹ 30 more rowsModificar base de datos
Curvas_amplif2 <- Curvas_amplif %>%
mutate(Ciclos = Cycle,
Manuel = A1,
Regina = B1,
Marian = C1,
Ricardo = D1,
Neto = E1,
Johan = H1) %>%
select(-Cycle:-H1) %>%
filter(Ciclos>=15)
Curvas_amplif2## # A tibble: 26 × 7
## Ciclos Manuel Regina Marian Ricardo Neto Johan
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 15 -1.05 20.7 6.85 2.70 -1.42 -7.33
## 2 16 -0.998 17.2 25.5 3.72 -1.68 -5.90
## 3 17 3.05 33.9 45.0 15.5 -6.40 -2.47
## 4 18 -1.90 49.6 82.2 31.1 -6.78 -4.23
## 5 19 -4.91 84.6 151. 56.1 -7.36 -9.54
## 6 20 -6.37 118. 241. 92.6 -4.65 -13.1
## 7 21 -8.76 172. 413. 174. -5.39 -10.6
## 8 22 -4.11 232. 623. 265. -7.50 -12.7
## 9 23 2.24 301. 886. 391. -7.09 -11.2
## 10 24 -2.40 372. 1180. 526. -7.93 -22.4
## # ℹ 16 more rowsReordenamiento de datos 1. Seleccionar datos a reordenar (variables dependientes) 2. Agrupar variables por nombre 3. Agrupar variables por ciclo
Curvas_amplif3 <- Curvas_amplif2 %>%
pivot_longer(cols = -Ciclos,
names_to = "Muestras",
values_to = "Fluorescencias")
Curvas_amplif3## # A tibble: 156 × 3
## Ciclos Muestras Fluorescencias
## <dbl> <chr> <dbl>
## 1 15 Manuel -1.05
## 2 15 Regina 20.7
## 3 15 Marian 6.85
## 4 15 Ricardo 2.70
## 5 15 Neto -1.42
## 6 15 Johan -7.33
## 7 16 Manuel -0.998
## 8 16 Regina 17.2
## 9 16 Marian 25.5
## 10 16 Ricardo 3.72
## # ℹ 146 more rowsGráfica
Gráfica_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 every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.Gráfica_amplif
Mejorar la gráfica
Umbral_ciclos <- 75
Gráfica_amplif2<-Gráfica_amplif +
geom_hline(yintercept = Umbral_ciclos,
linetype= "dashed",
color="#8B008B")+
theme_classic()+
labs(title= "Curvas de amplificacion RT-qPCR",
subtitle= "Todas las muestras",
caption= "Diseño: Ricardo Palos, Regina Hernández, Diego Campos",
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))+
scale_y_continuous(breaks =seq(min(Curvas_amplif3$Fluorescencias),
max(Curvas_amplif3$Fluorescencias),
by= 270),
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 every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.Gráfica_amplif2
Gráfica datos del equipo
Gráfica_amplif_equipo <- ggplot(Curvas_amplif2,
aes(x=Ciclos,
y=Ricardo)) +
geom_line(linewidth= 1, color= "#ADFF2F")+
geom_hline(yintercept = Umbral_ciclos,
linetype= "dashed",
color="#8B008B")+
theme_classic()+
labs(title= "Curvas de amplificacion RT-qPCR",
subtitle= "Muestra equipo RRD",
caption= "Diseño: Ricardo Palos, Regina Hernández, Diego Campos",
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))+
scale_y_continuous(breaks =seq(min(Curvas_amplif3$Fluorescencias),
max(Curvas_amplif3$Fluorescencias),
by= 300),
labels = scales::number_format(accuracy = 0.05))
Gráfica_amplif_equipo
Gráfica del equipo comparada con Profesor (Manuel)
Gráfica_amplif_equipo_prof <- ggplot(Curvas_amplif2,
aes(x=Ciclos)) +
geom_line(aes ( y= Ricardo, color = "Ricardo"), linewidth= 1) +
geom_line(aes ( y= Manuel, color = "Manuel"), linewidth= 1) +
geom_hline(yintercept = Umbral_ciclos,
linetype= "dashed",
color="#8B008B")+
scale_color_manual(values = c("Ricardo" = "#ADFF2F", "Manuel" = "#48D1CC")) +
theme_classic()+
labs(title= "Curvas de amplificacion RT-qPCR",
subtitle= "Comparación de muestras",
caption= "Diseño: Ricardo Palos, Regina Hernández, Diego Campos",
x= "Ciclos",
y= "Fluorescencia (u.a.)",
color = "Equipos")+
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))+
scale_y_continuous(breaks =seq(min(Curvas_amplif3$Fluorescencias),
max(Curvas_amplif3$Fluorescencias),
by= 300),
labels = scales::number_format(accuracy = 0.05)) +
geom_line(aes(x = Ciclos,
y= Manuel),
color = "#48D1CC",
linewidth = 1.5)
Gráfica_amplif_equipo_prof