Gráficos librería echarts4r

Librerías

• pedigreemm: Conjunto de datos
• dplyr: Manipulación de datos
• echarts4r : Graficación

library(pedigreemm)
library(dplyr)
library(echarts4r)
klippy::klippy()

Conjunto de datos

Descripción

Registros de la producción de leche de 3397 lactancias desde la primera hasta la cincuentena Holstein de parto. Estas fueron 1,359 vacas, hijas de 38 toros en 57 hatos. Los datos se descargaron del sitio de Internet del USDA. Todos los registros de lactancia representan vacas con al menos 100 días en leche, con un promedio de 347 días. La producción de leche varió de 4.065 a 19.345 kg estimada para 305 días, con un promedio de 11.636 kg. Hubo 1.314, 1.006, 640, 334 y 103 registros de animales de primera a quinta lactancia

Formato

Un marco de datos con 3397 observaciones sobre las siguientes 9 variables.

• id: Identificador numérico de la vaca
• lact: Número de lactancias para las que se mide la producción
• herd: hato
• sire: Padre
• dim: Número de días en leche para esa lactancia
• milk: Producción de leche estimada en 305 días
  
• fat: Producción de grasa estimada en 305 días
• prot: Producción de proteínas estimada en 305 días
  
• scs: Puntuación de células somáticas

Milk <- milk %>%
  mutate(lact = factor(lact))

Milk

Exploración

Boxplot

Número de días en leche

Milk %>%
  e_charts() %>%
  e_boxplot(dim, outliers = FALSE) %>%
  e_visual_map(scale = e_scale,
               inRange = list(color = c("#edafda", "#eeeeee", "#59c4e6"))) %>%
  e_image_g(
    left = 90,
    top = -15,
    z = -999,
    style = list(
      image = "https://st3.depositphotos.com/1027110/36470/v/450/depositphotos_364707606-stock-illustration-holstein-friesian-cow-breeds-of.jpg",
      width = 90,
      height = 90,
      opacity = 0.8
    )
  ) %>%
  e_tooltip(trigger = "axis")

Producción proteina por lactancia

Milk %>% 
  group_by(lact) %>% 
  e_charts() %>% 
  e_boxplot(prot, itemStyle = list(color = "#77db75" , 
                                   opacity = 0.5)) %>%
  e_tooltip(trigger = "axis") %>%
 #e_visual_map(scale = e_scale,  itemStyle = list(color = "blue")) %>%
  e_image_g(
    left = 110,
    top = -15,
    z = -999,
    style = list(
      image = "https://st3.depositphotos.com/1027110/36470/v/450/depositphotos_364707606-stock-illustration-holstein-friesian-cow-breeds-of.jpg",
      width = 90,
      height = 90,
      opacity = 0.8
    )
  ) %>% 
  e_axis_labels(x = "Lactancia", y = "Proteina") 

Histograma

Distribución de la producción de leche

Milk %>%
  e_charts() %>%
  e_histogram(milk, name = "Histograma") %>%
  e_density(
    milk,
    areaStyle = list(opacity = 0.4),
    smooth = TRUE,
    name = "Densidad",
    y_index = 1
  ) %>%
  e_tooltip(trigger = "axis") %>%
  e_mark_line(
    data = list(xAxis = mean(Milk$milk)),
    title = "Media",
    itemStyle = list(color = "darkred")
  ) %>%
  e_image_g(
    left = 100,
    top = -15,
    z = -999,
    style = list(
      image = "https://st3.depositphotos.com/1027110/36470/v/450/depositphotos_364707606-stock-illustration-holstein-friesian-cow-breeds-of.jpg",
      width = 90,
      height = 90,
      opacity = 0.8
    )
  )

Dispersión

Contenido grasa según la producción de leche y proteina

Diagrama de dispersión de un solo eje (singleAxis)

Milk %>%
  mutate(Grasa = fat) %>%
  e_charts(milk, height = 200) %>%
  e_single_axis(bottom = 40) %>%
  e_scatter(Grasa, # Valor
            prot, # Tamaño círculos
            coord_system = "singleAxis") %>%
  e_legend(left = "left", bottom = "center")  %>%
  e_tooltip(formatter = e_tooltip_pointer_formatter("currency"),
            axisPointer = list(type = "cross")) %>%
  e_datazoom(x_index = 0) %>%
  e_image_g(
    left = 70,
    top = -15,
    z = -999,
    style = list(
      image = "https://st3.depositphotos.com/1027110/36470/v/450/depositphotos_364707606-stock-illustration-holstein-friesian-cow-breeds-of.jpg",
      width = 90,
      height = 90,
      opacity = 0.8
    )
  )

Producción leche y proteina

Milk %>%
  e_charts(milk) %>%
  e_scatter(prot, symbol_size = 8) %>%
  e_tooltip(formatter = e_tooltip_pointer_formatter("currency"),
            axisPointer = list(type = "cross")) %>%
  e_axis_labels(x = "Leche", y = "Proteina") %>%
  e_datazoom(x_index = 0, type = "slider") %>%
  e_legend(FALSE) %>%
  e_image_g(
    left = 100,
    top = -15,
    z = -999,
    style = list(
      image = "https://st3.depositphotos.com/1027110/36470/v/450/depositphotos_364707606-stock-illustration-holstein-friesian-cow-breeds-of.jpg",
      width = 90,
      height = 90,
      opacity = 0.8
    )
  )

Relación producción leche y contenido de grasa

Milk %>%
  e_charts(milk) %>%
  e_scatter(fat, name = "Grasa") %>%
  e_axis_labels(x = "Leche",
                y = "Grasa") %>%
  e_lm(fat ~ milk, name = "Regresión Lineal") %>%
  e_tooltip(formatter = e_tooltip_pointer_formatter("currency"),
            axisPointer = list(type = "cross")) %>% 
  e_datazoom(x_index = 0, type = "slider")  %>%
  e_image_g(
    left = 95,
    top = -15,
    z = -999,
    style = list(
      image = "https://st3.depositphotos.com/1027110/36470/v/450/depositphotos_364707606-stock-illustration-holstein-friesian-cow-breeds-of.jpg",
      width = 90,
      height = 90,
      opacity = 0.8
    )
  ) 

Relación entre contenido de proteina y células somáticas con el número de días en leche

Milk %>%
  mutate(DIM = dim,
         SCS = scs,
         Proteina = prot) %>%
  e_charts(DIM) %>%
  e_scatter(Proteina, SCS) %>%
  e_effect_scatter(SCS, Proteina, y_index = 1) %>%
  e_grid(index = c(0, 1)) %>%
  e_tooltip() %>%
  e_image_g(
    left = 95,
    top = -15,
    z = -999,
    style = list(
      image = "https://st3.depositphotos.com/1027110/36470/v/450/depositphotos_364707606-stock-illustration-holstein-friesian-cow-breeds-of.jpg",
      width = 90,
      height = 90,
      opacity = 0.8
    )
  )

Gráfico barras

Producción leche por hato

Milk %>%
  mutate(Leche = milk) %>% 
  e_charts(herd) %>%
  e_bar(Leche) %>% 
  e_axis_labels(x = "Hato", y = " ") %>% 
  e_tooltip(formatter = e_tooltip_pointer_formatter("currency"),
            axisPointer = list(type = "cross")) %>% 
    e_image_g(
    left = 95,
    top = -15,
    z = -999,
    style = list(
      image = "https://st3.depositphotos.com/1027110/36470/v/450/depositphotos_364707606-stock-illustration-holstein-friesian-cow-breeds-of.jpg",
      width = 90,
      height = 90,
      opacity = 0.8
    )
  )

Promedio células somáticas por lactancia

Milk %>% group_by(lact, scs) %>%
  summarise(promedio = mean(milk)) %>% 
  e_charts(lact) %>%
  e_bar(promedio,  stack = "grp") %>% 
  e_axis_labels(x = "Lactancia", y = "SCS") %>% 
  e_tooltip(formatter = e_tooltip_pointer_formatter("currency"),
            axisPointer = list(type = "cross")) %>% 
    e_image_g(
    left = 95,
    top = -15,
    z = -999,
    style = list(
      image = "https://st3.depositphotos.com/1027110/36470/v/450/depositphotos_364707606-stock-illustration-holstein-friesian-cow-breeds-of.jpg",
      width = 90,
      height = 90,
      opacity = 0.8
    )
  )

Grasa y proteina por lactancia

Milk %>%
  mutate(Grasa = fat,
         Proteina = prot) %>%
  e_charts(lact) %>%
  e_bar(Proteina, stack = "grp") %>%
  e_bar(Grasa, stack = "grp") %>%
  e_axis_labels(x = "Lactancia", y = " ")  %>%
  e_tooltip(formatter = e_tooltip_pointer_formatter("currency"),
            axisPointer = list(type = "cross")) %>%
  e_image_g(
    left = 95,
    top = -15,
    z = -999,
    style = list(
      image = "https://st3.depositphotos.com/1027110/36470/v/450/depositphotos_364707606-stock-illustration-holstein-friesian-cow-breeds-of.jpg",
      width = 90,
      height = 90,
      opacity = 0.8
    )
  )

Días en leche y recuento células somáticas según el padre (Promedios)

Milk %>%
  group_by(sire) %>%
  summarise(DIM = mean(prot),
            SCS = mean(dim)) %>%
  e_charts(sire) %>%
  e_bar(DIM) %>%
  e_step(SCS) %>%
  e_axis_labels(x = "Padre") %>%
  e_image_g(
    left = 95,
    top = -15,
    z = -999,
    style = list(
      image = "https://st3.depositphotos.com/1027110/36470/v/450/depositphotos_364707606-stock-illustration-holstein-friesian-cow-breeds-of.jpg",
      width = 90,
      height = 90,
      opacity = 0.8
    )
  ) %>%
  e_tooltip(formatter = e_tooltip_pointer_formatter("currency"),
            axisPointer = list(type = "cross")) %>%
  e_datazoom()

Grafico de lineas

Promedio células somáticas según el padre

Milk %>%
  group_by(sire) %>%
  summarise(
    `Promedio csc` = mean(scs),
    scs_1 = mean(scs) - sd(scs),
    scs_2 = mean(scs) + sd(scs)
  ) %>%
  e_charts(sire) %>%
  e_line(`Promedio csc`) %>%
  e_band(scs_1, scs_2) %>%
  e_axis_labels(x = "Padre", y = "CSC") %>%
  e_tooltip(axisPointer = list(type = "cross")) %>%
  e_datazoom(x_index = 0, type = "slider") %>%
  e_image_g(
    left = 95,
    top = -15,
    z = -999,
    style = list(
      image = "https://st3.depositphotos.com/1027110/36470/v/450/depositphotos_364707606-stock-illustration-holstein-friesian-cow-breeds-of.jpg",
      width = 90,
      height = 90,
      opacity = 0.8
    )
  )

Producción de leche y contenido de grasa por lactancia

Milk %>%
  group_by(lact) %>%
  e_charts(milk) %>%
  e_line(fat) %>%
  e_facet(rows = 3,
          cols = 2,
          legend_space = 12) %>%
  e_image_g(
    left = 55,
    top = -15,
    z = -999,
    style = list(
      image = "https://st3.depositphotos.com/1027110/36470/v/450/depositphotos_364707606-stock-illustration-holstein-friesian-cow-breeds-of.jpg",
      width = 90,
      height = 90,
      opacity = 0.8
    )
  ) %>%
  e_axis_labels(x = "Leche", y = "Grasa") 

Promedio contenido de grasa y proteina según el hato

Milk %>%
  group_by(herd) %>%
  summarise(
    Grasa = mean(fat),
    Proteina = mean(prot)
  ) %>%
  e_charts(herd) %>%
  e_line(Grasa) %>%
  e_area(Proteina) %>%
  e_axis_labels(x = "Hato") %>%
  e_image_g(
    left = 95,
    top = -15,
    z = -999,
    style = list(
      image = "https://st3.depositphotos.com/1027110/36470/v/450/depositphotos_364707606-stock-illustration-holstein-friesian-cow-breeds-of.jpg",
      width = 90,
      height = 90,
      opacity = 0.8
    )
  ) %>%
  e_y_axis(nameLocation = "center",
           axisPointer = list(type = "dotted")) %>%
  e_datazoom(y_index = 0, type = "slider")

Gráfico correlación

Milk %>%
  select(where(is.numeric)) %>%
  mutate(
    DIM = dim,
    Leche = milk,
    Grasa = fat,
    Proteina = prot,
    SCS = scs
  ) %>%
  select(-c(1:5)) %>%
  cor() %>%
  e_charts() %>%
  e_correlations(order = "hclust",
                 inRange = list(color = c("#edafda", "#eeeeee", "#59c4e6"))) %>%
  e_tooltip() %>%
  e_image_g(
    left = 75,
    top = -15,
    z = -999,
    style = list(
      image = "https://st3.depositphotos.com/1027110/36470/v/450/depositphotos_364707606-stock-illustration-holstein-friesian-cow-breeds-of.jpg",
      width = 90,
      height = 90,
      opacity = 0.8
    )
  )

Gráfico paralelo

Promedio proteina, grasas y células somáticas por lactancia

Milk %>%
  group_by(lact) %>%
  summarise(
    Leche = mean(milk),
    Grasa = mean(fat),
    Proteina = mean(prot),
    CSC = mean(scs),
  ) %>% 
  mutate(Lact = lact) %>% 
  e_charts() %>%
  e_parallel(Lact,
             Leche,
             Grasa,
             Proteina,
             CSC,
            opts = list(smooth = TRUE)) %>%
  e_image_g(
    left = 95,
    top = -15,
    z = -999,
    style = list(
      image = "https://st3.depositphotos.com/1027110/36470/v/450/depositphotos_364707606-stock-illustration-holstein-friesian-cow-breeds-of.jpg",
      width = 90,
      height = 90,
      opacity = 0.8
    )
  ) %>% 
  e_tooltip(axisPointer = list(type = "cross"))

• Referencias:

  • echarts4r

  • Apache ECharts

  • Notas sobre cómo dibujar un gráfico de líneas con el paquete echarts4r en R

  • LatinR 2020