I have got this code that is in R Markdown and uses plotly. I want to add a limit on Y axis. Here it uses the maximum of "est" variables but I want to put a cut off of 10. I understand that this would affect the confidence interval (upper and lower) as well.

I have provided the data using dput() here. Hope this is the right way as its first time using this function. dput(plot_data)

structure(list(quarter = structure(c(2014.25, 2015.5, 2015.75, 
2016, 2016.25, 2016.5, 2016.75, 2017, 2017.25, 2017.5, 2017.75, 
2018, 2018.25, 2018.5, 2018.75, 2019, 2019.25, 2019.5, 2019.75, 
2020, 2020.25, 2020.5, 2020.75, 2021, 2021.25, 2021.75), class = "yearqtr"), 
    cases = c(1L, 1L, 38L, 4L, 2L, 8L, 9L, 13L, 6L, 20L, 32L, 
    42L, 26L, 18L, 25L, 11L, 5L, 4L, 4L, 3L, 1L, 2L, 2L, 2L, 
    3L, 1L), est = c(0, 0, 0, 21, 0.153846153846154, 0.238095238095238, 
    2.83333333333333, 2.2, 1.11764705882353, 1.18181818181818, 
    2.73684210526316, 2.84615384615385, 1.30769230769231, 0.594594594594595, 
    0.632352941176471, 0.818181818181818, 0.372093023255814, 
    0.25, 0.5, 0.777777777777778, 0.5, 0.428571428571429, 1, 
    1.33333333333333, 1.25, 1), lower = c(0, 0, 0, 9.36875, 0.0605698529411765, 
    0.0900568181818182, 1.24583333333333, 1.0825, 0.537, 0.704503105590062, 
    1.88461538461538, 1.96911764705882, 0.914764492753623, 0.402261904761905, 
    0.390400682011935, 0.539913043478261, 0.224595551061679, 
    0.103584229390681, 0.213787185354691, 0.25, 0.105277777777778, 
    0, 0.1825, 0.0950000000000005, 0.2, 0.154166666666667), upper = c(0, 
    0, 0, 9, 0.287045454545454, 0.448195187165775, 9, 4.98499999999999, 
    2.49523809523809, 2.1875, 4.5, 4.60504201680672, 1.88531641397495, 
    0.867572463768115, 0.869867374005305, 1.35281440162272, 0.629361179361179, 
    0.457125307125307, 1.09090909090909, 2.17285714285714, 3, 
    2.68333333333333, 9, 9, 7.52499999999999, 6)), row.names = c(NA, 
-26L), class = c("tbl_df", "tbl", "data.frame"))

plot_data <- tibble(
    
    quarter = rp_list$infection_quarter,
    cases = rp_list$cases,
    est = edr_frame$est,
    lower = edr_frame$lower,
    upper = edr_frame$upper
  ) %>% 
    mutate (upper = case_when(upper >= 10 ~9,
                              upper >= 9 ~ 8,
                              TRUE ~ upper))
  
  plot_edr <- plot_data %>%
    # Dashed line for upper CI
    plotly::plot_ly(
      name = "95% CI (upper)",
      type = 'scatter',
      mode = 'lines',
      x = ~quarter,
      y = ~upper,
      line = list(
        dash = "dot",
        color = c("#A8B9CB")
      )
    ) %>%
    add_trace(
      name = "95% CI (lower)",
      type = 'scatter',
      mode = 'lines',
      x = ~quarter,
      y = ~lower,
      line = list(
        dash = "dot",
        color = c("#A8B9CB")
      )
    ) %>%
    add_trace(
      name = "EDR",
      type = 'scatter',
      mode = 'lines',
      x = ~quarter,
      y = ~est,
      line = list(
        dash = "line",
        color = c("#2F3D70")
      )
    ) %>%
    layout(
      title = 'Ratio',
     
      xaxis = list(title = "Quarter"),
      yaxis = list(title = "Ratio with 95% CI"),
      
      shapes = list(
        list(type = "rect",
             fillcolor = "green", line = list(color = "green"), opacity = 0.1,
             x0 = min(plot_data$quarter), x1 = max(plot_data$quarter), xref = "x",
             y0 = 0, y1 = 1, yref = "y"),
        list(type = "rect",
             fillcolor = "red", line = list(color = "red"), opacity = 0.1,
             x0 = min(plot_data$quarter), x1 = max(plot_data$quarter), xref = "x",
             y0  = 1, y1 = max(plot_data$upper), yref = "y1")))

Many Thanks

CodePudding user response：

You should add range = c(0,10) to your yaxis in your layout the plot. You can use the following code:

library(plotly)
library(tidyverse)
plot_edr <- plot_data %>%
  # Dashed line for upper CI
  plotly::plot_ly(
    name = "95% CI (upper)",
    type = 'scatter',
    mode = 'lines',
    x = ~quarter,
    y = ~upper,
    line = list(
      dash = "dot",
      color = c("#A8B9CB")
    )
  ) %>%
  add_trace(
    name = "95% CI (lower)",
    type = 'scatter',
    mode = 'lines',
    x = ~quarter,
    y = ~lower,
    line = list(
      dash = "dot",
      color = c("#A8B9CB")
    )
  ) %>%
  add_trace(
    name = "EDR",
    type = 'scatter',
    mode = 'lines',
    x = ~quarter,
    y = ~est,
    line = list(
      dash = "line",
      color = c("#2F3D70")
    )
  ) %>%
  layout(
    title = 'Ratio',
    
    xaxis = list(title = "Quarter"),
    yaxis = list(title = "Ratio with 95% CI", range = c(0,10)),
    
    shapes = list(
      list(type = "rect",
           fillcolor = "green", line = list(color = "green"), opacity = 0.1,
           x0 = min(plot_data$quarter), x1 = max(plot_data$quarter), xref = "x",
           y0 = 0, y1 = 1, yref = "y"),
      list(type = "rect",
           fillcolor = "red", line = list(color = "red"), opacity = 0.1,
           x0 = min(plot_data$quarter), x1 = max(plot_data$quarter), xref = "x",
           y0  = 1, y1 = max(plot_data$upper), yref = "y1")))

Output: