if(!require(pacman))
install.packages("pacman")
## Loading required package: pacman
library("pacman")
p_load("vroom",
"dplyr",
"ggplot2",
"tidyr",
"ggrepel",
"plotly")
Melting_curve <-vroom (file= "https://raw.githubusercontent.com/ManuelLaraMVZ/resultados_PCR_practica/refs/heads/main/Disoci_ejemplo1.csv")
## Rows: 55 Columns: 6
## āā Column specification āāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāā
## Delimiter: ","
## dbl (6): Temperature, A1, B1, C1, D1, E1
##
## ā¹ Use `spec()` to retrieve the full column specification for this data.
## ā¹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Melting_curve
## # A tibble: 55 Ć 6
## Temperature A1 B1 C1 D1 E1
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 65 1.96 1.98 2.11 2.11 0.0869
## 2 65.5 1.94 1.99 2.06 2.08 0.0834
## 3 66 1.89 1.93 2.03 2.07 0.0932
## 4 66.5 1.86 1.89 1.98 2.02 0.0676
## 5 67 1.82 1.89 1.94 1.98 0.0738
## 6 67.5 1.77 1.83 1.90 1.93 0.0766
## 7 68 1.74 1.78 1.86 1.87 0.0686
## 8 68.5 1.70 1.76 1.79 1.84 0.0689
## 9 69 1.65 1.71 1.79 1.80 0.0665
## 10 69.5 1.60 1.64 1.75 1.76 0.0744
## # ā¹ 45 more rows
Melting_curve2 <- Melting_curve %>%
mutate(Temperatura=Temperature,DDR=A1,JRWF=B1,PPOF=C1,MLL=D1,H2O=E1)%>%
select(-Temperature:-E1)
Melting_curve2
## # A tibble: 55 Ć 6
## Temperatura DDR JRWF PPOF MLL H2O
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 65 1.96 1.98 2.11 2.11 0.0869
## 2 65.5 1.94 1.99 2.06 2.08 0.0834
## 3 66 1.89 1.93 2.03 2.07 0.0932
## 4 66.5 1.86 1.89 1.98 2.02 0.0676
## 5 67 1.82 1.89 1.94 1.98 0.0738
## 6 67.5 1.77 1.83 1.90 1.93 0.0766
## 7 68 1.74 1.78 1.86 1.87 0.0686
## 8 68.5 1.70 1.76 1.79 1.84 0.0689
## 9 69 1.65 1.71 1.79 1.80 0.0665
## 10 69.5 1.60 1.64 1.75 1.76 0.0744
## # ā¹ 45 more rows
Melting_curve3 <- Melting_curve2 %>%
pivot_longer(cols = -Temperatura,
names_to = "Muestras",
values_to = "Fluorescencia")
Melting_curve3
## # A tibble: 275 Ć 3
## Temperatura Muestras Fluorescencia
## <dbl> <chr> <dbl>
## 1 65 DDR 1.96
## 2 65 JRWF 1.98
## 3 65 PPOF 2.11
## 4 65 MLL 2.11
## 5 65 H2O 0.0869
## 6 65.5 DDR 1.94
## 7 65.5 JRWF 1.99
## 8 65.5 PPOF 2.06
## 9 65.5 MLL 2.08
## 10 65.5 H2O 0.0834
## # ā¹ 265 more rows
Grafica_melting <- ggplot(Melting_curve3,
aes(x = Temperatura,
y = Fluorescencia,
color = Muestras))+
geom_line(linewidth=1.5)
Grafica_melting
Derivadas <- Melting_curve2 %>%
mutate(across(DDR:H2O,
~-c(NA, diff(.x)/diff(Melting_curve2$Temperatura)), .names ="d_{.col}")) %>%
select(-DDR: -H2O) %>%
slice(-1)
Derivadas
## # A tibble: 54 Ć 6
## Temperatura d_DDR d_JRWF d_PPOF d_MLL d_H2O
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 65.5 0.0365 -0.0147 0.0940 0.0711 0.00703
## 2 66 0.102 0.108 0.0614 0.0146 -0.0197
## 3 66.5 0.0695 0.0883 0.112 0.108 0.0512
## 4 67 0.0652 0.00898 0.0646 0.0772 -0.0123
## 5 67.5 0.109 0.114 0.0903 0.0923 -0.00567
## 6 68 0.0666 0.0994 0.0707 0.122 0.0162
## 7 68.5 0.0774 0.0335 0.139 0.0558 -0.000754
## 8 69 0.0860 0.0979 -0.00165 0.0850 0.00488
## 9 69.5 0.111 0.146 0.0908 0.0844 -0.0159
## 10 70 0.0582 0.0279 0.130 0.0864 0.00967
## # ā¹ 44 more rows
Derivadas2 <- Derivadas%>%
pivot_longer(cols = -Temperatura,
names_to = "Muestras",
values_to = "Derivadas")
Derivadas2
## # A tibble: 270 Ć 3
## Temperatura Muestras Derivadas
## <dbl> <chr> <dbl>
## 1 65.5 d_DDR 0.0365
## 2 65.5 d_JRWF -0.0147
## 3 65.5 d_PPOF 0.0940
## 4 65.5 d_MLL 0.0711
## 5 65.5 d_H2O 0.00703
## 6 66 d_DDR 0.102
## 7 66 d_JRWF 0.108
## 8 66 d_PPOF 0.0614
## 9 66 d_MLL 0.0146
## 10 66 d_H2O -0.0197
## # ā¹ 260 more rows
Grafica_derivada <-ggplot(Derivadas2,
aes(x = Temperatura,
y = Derivadas,
color = Muestras)) +
geom_line(linewidth=1.5)+
theme_classic()+
labs(title = "Curvas de la derivada de disociaciĆ³n RT-qPCR",
subtitle = "Todas las muestras",
caption = "DiseĆ±Ć³:Paola LĆ³pez",
x = "Temperatura (Ā°C)",
y = expression("-" * Delta * "F/" * Delta * "T"))+
theme(axis.line = element_line(size = 1.2, color = "black"),
axis.title = element_text(face = "bold"),
axis.text = element_text(face = "bold"))+
scale_x_continuous(breaks=seq(min(Derivadas2$Temperatura),
max(Derivadas2$Temperatura),
by = 2.5))
## Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
## ā¹ Please use the `linewidth` argument instead.
## This warning is displayed once per session.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
Grafica_derivada
Grafica_derivada_3D <- plot_ly(Derivadas2,
x = ~Temperatura,
y = ~Muestras,
z = ~Derivadas,
color = ~factor(Muestras),
type = "scatter3d",
mode = "lines",
line = list(width = 6)) %>%
layout(title= "Curva de derivada en 3D",
scene= list(
xaxis=list(title="Temperatura"),
yaxis=list(title="Muestras"),
zaxis=list(title="-dT/dF")))
Grafica_derivada_3D
Grafica_derivada_equipo <- ggplot(Derivadas,
aes(x = Temperatura))+
geom_line(aes(y=d_MLL,color="d_MLL"),linewidth = 1.5)+
geom_line(aes(y=d_H2O,color="d_H2O"),linewidth = 1.5)+
scale_color_manual(values=c("d_MLL"="#6287f1","d_H2O"="pink"))+
theme_classic() +
labs(title = "Derivada de disociaciĆ³n RT-qPCR",
subtitle = "Tejido: Corteza de cerebro",
caption = "DiseĆ±Ć³:Paola LĆ³pez",
x = "Temperatura (Ā° C)",
y = expression(-Delta~F/Delta~T))+
theme(
axis.line = element_line(size = 1.2, color = "black"),
axis.title = element_text(face = "bold"),
axis.text = element_text(face = "bold"),
legend.title = element_text(face = "bold"),
legend.text = element_text(face = "bold")) +
scale_x_continuous(breaks = seq(min(Derivadas$Temperatura), max(Derivadas$Temperatura), by = 2.5))
Grafica_derivada_equipo
Pico <- max(Derivadas$d_MLL)
Pico
## [1] 0.738565
Tm <- Derivadas %>%
filter(d_MLL==Pico)%>%
select(Temperatura,d_MLL)
Tm
## # A tibble: 1 Ć 2
## Temperatura d_MLL
## <dbl> <dbl>
## 1 82 0.739
Grafica_derivada_equipo2 <- Grafica_derivada_equipo+
geom_vline(xintercept=Tm$Temperatura,
color="purple",
linetype="dashed",
linewidth=1)+
geom_label_repel(data=Tm,
aes(x=Temperatura,
y=d_MLL,
label=paste("Tm=",round(Temperatura),"Ā°C")),
nudge_x=4,
nudge_y=-0.03,
max.overlaps=100,
color="black",
fill="lightgreen")
Grafica_derivada_equipo2
