if(!require(pacman))
install.packages("pacman")
## Loading required package: pacman
install.packages("dyplr")
## Installing package into '/cloud/lib/x86_64-pc-linux-gnu-library/4.4'
## (as 'lib' is unspecified)
## Warning: package 'dyplr' is not available for this version of R
##
## A version of this package for your version of R might be available elsewhere,
## see the ideas at
## https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
library("pacman")
library("dplyr")
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
p_load("vroom",
"dyplyr",
"ggplot2",
"tidyr")
## Installing package into '/cloud/lib/x86_64-pc-linux-gnu-library/4.4'
## (as 'lib' is unspecified)
## Warning: package 'dyplyr' is not available for this version of R
##
## A version of this package for your version of R might be available elsewhere,
## see the ideas at
## https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
## Warning: 'BiocManager' not available. Could not check Bioconductor.
##
## Please use `install.packages('BiocManager')` and then retry.
## Warning in p_install(package, character.only = TRUE, ...):
## Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
## logical.return = TRUE, : there is no package called 'dyplyr'
## Warning in p_load("vroom", "dyplyr", "ggplot2", "tidyr"): Failed to install/load:
## dyplyr
Curvas_amplif<- vroom(file="https://raw.githubusercontent.com/ManuelLaraMVZ/resultados_PCR_practica/refs/heads/main/Amplif_grupo1_24022025.csv")
## `curl` package not installed, falling back to using `url()`
## Rows: 51 Columns: 9
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## dbl (9): Cycle, A1, B1, C1, D1, E1, F1, G1, Manuel
##
## 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 A1 B1 C1 D1 E1 F1 G1 Manuel
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 1 -732. -450. -50.4 -30.1 -109. -10.7 -5.87 -37.4
## 2 2 -402. -237. -20.8 15.9 -80.6 -10.4 -8.17 1.12
## 3 3 -294. -171. -14.1 11.9 -71.2 -7.35 -5.06 7.85
## 4 4 -322. -143. 8.14 13.6 -60.4 -6.83 -3.26 15.0
## 5 5 -300. -100. 12.1 5.93 -54.7 -3.67 -3.51 8.92
## 6 6 -277. -84.8 17.0 14.6 -41.4 1.04 0.0908 6.62
## 7 7 -232. -78.9 14.0 10.8 -31.2 -2.24 -2.85 -4.64
## 8 8 -197. -61.4 14.8 13.6 -23.1 3.22 4.79 -2.66
## 9 9 -143. -39.9 11.0 10.4 -13.4 4.09 2.17 -4.38
## 10 10 -95.6 -12.9 3.21 8.78 -2.80 2.80 -0.0460 28.3
## # ℹ 41 more rows
Curvas_amplif2<- Curvas_amplif %>%
mutate(Ciclos = Cycle,
PPBA = A1,
ZARX = B1,
FFSS= C1,
LANS = D1,
NEGATIVO = E1,
D2MI = F1,
Control = Manuel) %>%
select(-Cycle:-Manuel)%>%
filter(Ciclos>=6)
Curvas_amplif2
## # A tibble: 46 × 8
## Ciclos PPBA ZARX FFSS LANS NEGATIVO D2MI Control
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 6 -277. -84.8 17.0 14.6 -41.4 1.04 6.62
## 2 7 -232. -78.9 14.0 10.8 -31.2 -2.24 -4.64
## 3 8 -197. -61.4 14.8 13.6 -23.1 3.22 -2.66
## 4 9 -143. -39.9 11.0 10.4 -13.4 4.09 -4.38
## 5 10 -95.6 -12.9 3.21 8.78 -2.80 2.80 28.3
## 6 11 -78.1 -13.1 2.47 1.01 0.325 0.486 97.9
## 7 12 -35.1 -1.24 -3.91 2.81 9.72 1.88 242.
## 8 13 -44.5 1.21 7.42 -0.884 13.2 -5.39 523.
## 9 14 4.89 11.1 28.0 7.84 21.5 -0.898 1007.
## 10 15 16.6 11.7 57.1 16.4 26.2 0.640 1841.
## # ℹ 36 more rows
Curvas_amplif3 <- Curvas_amplif2%>%
pivot_longer(cols= -Ciclos,
names_to = "Muestras",
values_to = "Fluorescencias" )
Curvas_amplif3
## # A tibble: 322 × 3
## Ciclos Muestras Fluorescencias
## <dbl> <chr> <dbl>
## 1 6 PPBA -277.
## 2 6 ZARX -84.8
## 3 6 FFSS 17.0
## 4 6 LANS 14.6
## 5 6 NEGATIVO -41.4
## 6 6 D2MI 1.04
## 7 6 Control 6.62
## 8 7 PPBA -232.
## 9 7 ZARX -78.9
## 10 7 FFSS 14.0
## # ℹ 312 more rows
Grafica_amplif<- ggplot(data = Curvas_amplif3,
mapping = aes(x=Ciclos,
y=Fluorescencias,
colour = Muestras))+
geom_line (linewidth=1.5)
Grafica_amplif
Umbral_ciclos<- 300
Grafica_amplif2<- Grafica_amplif+
geom_hline(yintercept = Umbral_ciclos, linetype = "dashed", color="#1e2bf9")+
theme_classic()+
labs(title = "Curvas de aamplificación RT-qPCR",
subtitle = "Todas las muestras",
caption = "Diseñaron: FFSS",
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=10))+
scale_y_continuous(breaks = seq(min(Curvas_amplif3$Fluorescencias),
max(Curvas_amplif3$Fluorescencias),
by=1500),
labels = scales::number_format(accuracy = 1500))
## 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.
Grafica_amplif2
Grafica_amplif_equipo <- ggplot(Curvas_amplif2, aes(x = Ciclos)) +
geom_line(aes(y = FFSS, color = "FFSS"), linewidth = 1.2) +
geom_line(aes(y = NEGATIVO, color = "Negativo"), linewidth = 1.2) +
geom_line(aes(y = Control, color = "Control"), linewidth = 1.2) +
geom_hline(yintercept = Umbral_ciclos, linetype = "dashed", color = "#1e2bf9") +
theme_classic() +
labs(title = "Curvas de Amplificación RT-qPCR",
subtitle = "Todas las muestras",
caption = "Diseñaron: FFSS",
x = "Ciclos",
y = "Fluorescencia (u.a.)",
color = "Muestras") + # Agregar título a la leyenda
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 = 1000),
labels = scales::number_format(accuracy = 1000)) +
scale_color_manual(values = c("Negativo" = "#55f5cc",
"Control" = "#041b9b",
"FFSS" = "#70044e"))
Grafica_amplif_equipo
