R plotly adding traces in a loop

Question

I'm trying to plot many traces on the same figure, thus needing to use a loop but it doesn't work, as you can see in the example below :

Fig3abis<-plot_ly(data=dataresults3ab,x=dataresults3ab[[1]])
    
    for(j in c(100,500,1000,1500))
    {
        #print(dataresults3ab[,j])
        Fig3abis <- add_trace(Fig3abis,
                       y=~dataresults3ab[,j],
                       name=paste("N1",as.character(j),sep = "_"),
                       type="scatter",
                       mode="markers",
                       marker=list(size=4,color="black"))
    }
    
    Fig3abis <- Fig3abis%>% layout(title="Bifurcation diagram for five species competing for five resources. Local minima and maxima of species 1, 
                         from t=2,000 to t=4,000 days, as a function of the half-saturation constant K41",
                             showlegend=F,
                             xaxis=list(title="Half-saturation constant K41, of species 1",range=c(0.1,0.5)),
                             yaxis=list(title="Abundancie of species 1",range=c(0,100)))

First Figure

As you can see there is a problem : the plot only show the last added trace.

When I try to plot each trace one by one, it works really well, as you can see bellow :

Fig3a <- plot_ly(data=dataresults3ab,x=dataresults3ab[[1]])
  
  Fig3a <- add_trace(Fig3a,
                        y=~dataresults3ab[,100],
                        name="N1_2",
                        type="scatter",
                        mode="markers",
                        marker=list(size=4,color="black"))%>%
           add_trace(Fig3a,
                       y=~dataresults3ab[,500],
                       name="N_3",
                       type="scatter",
                       mode="markers",
                       marker=list(size=4,color="black"))%>%
           add_trace(Fig3a,
                       y=~dataresults3ab[,1000],
                       name="N1_4",
                       type="scatter",
                       mode="markers",
                       marker=list(size=4,color="black"))%>%
            add_trace(Fig3a,
                       y=~dataresults3ab[,1500],
                       name="N1_5",
                       type="scatter",
                       mode="markers",
                       marker=list(size=4,color="black"))

  Fig3a <- Fig3a%>% layout(title="Bifurcation diagram for five species competing for five resources. Local minima and maxima of species 1, from t=2,000 to t=4,000 days, as a function of the half-saturation constant K41",
           showlegend=F,
           xaxis=list(title="Half-saturation constant K41, of species 1",range=c(0.1,0.5)),
           yaxis=list(title="Abundancie of species 1",range=c(0,100)))

Second Figure

I've been looking for solution for quite a while and this is not the first time this problem is submitted but none of the different answers worked for me (using evaluate for example)

Note: here I used a small loop and a small sample of traces but in the end I'd like to plot around 8000 traces.

The data I used is a simple data frame with the first column displaying the x axis and all of the other represent each trace that needs to be plotted

I'm not familair with plot_ly, but this may be a lazy evaluation problem. Try replacing your for loop with an lapply. (Or putting a print(Fig3abis) inside the for loop). Also, if plot_ly works with ggplot aesthetics, you could avoid any sort of loop by working with tidy data: pivot_longer will do the trick. — Limey
– Limey, Commented Jul 1, 2022 at 14:52
Possible duplicate of https://stackoverflow.com/questions/67413684/adding-layers-to-ggplots-works-but-adding-in-a-loop-does-not. — Limey
– Limey, Commented Jul 1, 2022 at 15:01
Hi @Limey your solution using lapply works really well thank you very much. Therefore I have antoher problem because the loop is showing the plot at each step, making the process very long (I'll need 8000 loops in total) is there a way to disable this ? (it is also printing the current loop in the console). I couldn't find where to do it in the documentation. Thanks again ! — ggeremy
– ggeremy, Commented Jul 4, 2022 at 8:32
That's a new question! Nevertheless: library(tidyverse); dfList <- lapply(1:3, function(x) tibble(x=rnorm(5), y=rnorm(5))); p <- lapply(dfList, function(d) d %>% ggplot() + geom_line(aes(x, y))) does not print a plot for each iteration of the loop for me. You can then see the plots with simply p. You've not shown your implementation of the lapply solution, so I cannot say more. I repeat my suggestion that you may well be better off working with long data. This may be an XY problem. — Limey
– Limey, Commented Jul 4, 2022 at 8:41

VvdL · Accepted Answer · 2022-07-01 14:20:56Z

0

I think you are overwriting Fig3abis with every loop instead of adding a trace. Try this inside your loop:

Fig3abis <- Fig3abis %>% add_trace(....

Fig3abis<-plot_ly(data=dataresults3ab,x=dataresults3ab[[1]])
  
  for(j in c(100,500,1000,1500))
  {
  #print(dataresults3ab[,j])
  Fig3abis <- Fig3abis %>% 
           add_trace(Fig3abis,
                     y=~dataresults3ab[,j],
                     name=paste("N1",as.character(j),sep = "_"),
                     type="scatter",
                     mode="markers",
                     marker=list(size=4,color="black"))
  }
  
  Fig3abis <- Fig3abis%>% layout(title="Bifurcation diagram for five species competing for five ressources. Local minima and maxima of species 1, 
                       from t=2,000 to t=4,000 days, as a function of the half-saturation constant K41",
                           showlegend=F,
                           xaxis=list(title="Half-saturation constant K41, of species 1",range=c(0.1,0.5)),
                           yaxis=list(title="Abundancie of species 1",range=c(0,100)))

answered Jul 1, 2022 at 14:20

VvdL

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ggeremy Over a year ago

Hi, I tried but it doesn't work but thanks anyway :)

ggeremy · Accepted Answer · 2022-07-06 14:53:05Z

0

As Limey suggest in the comments, the problem was due to a lazy avaluation problem. I solved it using a lapply loop instead of a for loop.

answered Jul 6, 2022 at 14:53

ggeremy

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