Producing a plot highlighting causal variants and reducing opacity of non-causual variants

📊 Plotly Python
1

I am new to plotly, but using this platform as my aim is to produce a plot with 8 different overlaying plots with multiple y axis. I am reviewing genotype data and producing a plot of -log10(p) against BP. My practice code works for the image with reducing opacity of non-causal variants. However as soon as I increase the number of results in my dataset >10 rows the code fails to work? Is there a reason for this in the package. Thank you kindly for advice

test data code;

log <- c(0.28777133, 0.540758335, 0.331055266, 1.068186296, 0.075669015, 0.042105513, 20.156767222, 6.144238628, 5.752272167)
opacity <- c(0.2,0.2,0.2,0.2,0.2,0.2,1,1,1)
data <- data.frame(BP, log, opacity)
data$highlight <- row.names(data) %in% c("7", "8", "9")   ###highlight possible causal variants in practice dataset


### Display plot
fig <- plot_ly(width = 1200, height = 600)
fig <- fig %>% add_trace(data= data, 
                         x = ~BP, 
                         y = ~log, 
                         color = ~highlight, 
                         name = "", 
                         mode = "markers", 
                         type = "scatter",
                         marker = list(size = 8), 
                         colors = c("purple", "red"),
                         opacity=opacity)
fig ```
# works with practice data

``` BP <- c(117068919, 117072803, 117074604, 117075231, 117076684, 117077326, 117078553, 117080817, 117083725, 117086188, 117086549, 117087412 )
log <- c(0.28777133, 0.540758335, 0.331055266, 1.068186296, 0.075669015, 0.042105513, 20.156767222, 6.144238628, 5.752272167, 0.042201225, 0.460923901, 0.450016389 )
data <- data.frame(BP, log)
data$highlight <- row.names(data) %in% c("1", "2", "3", "4", "5")   

data$opacity[data$highlight==F]<-0.2
data$opacity[data$highlight==T]<-1
table(data$highlight)

data2<-data[rev(order(data$opacity)),]
data2<-data2[1:10,]

fig <- plot_ly(width = 1200, height = 600)
fig <- fig %>% add_trace(data= Crohns2, 
                         x = ~BP, 
                         y = ~log, 
                         color = ~highlight, 
                         name = "", 
                         mode = "markers", 
                         type = "scatter",
                         marker = list(size = 8), 
                         colors = c("purple", "red"),
                         opacity=opacity)
fig  ### doesnt work with > 10 rows 

data3<-data[rev(order(data$opacity)),]
data3<-data3[1:9,]

fig <- plot_ly(width = 1200, height = 600)
fig <- fig %>% add_trace(data= data3, 
                         x = ~BP, 
                         y = ~log, 
                         color = ~highlight, 
                         name = "", 
                         mode = "markers", 
                         type = "scatter",
                         marker = list(size = 8), 
                         colors = c("purple", "red"),
                         opacity=opacity)
fig ```  ## does work with 9 rows
2

Hi @victoria welcome to the forums.

You tagged your post with Plotly Python but the code you provided seems to be a different language.

Maybe you could use a different tag which corresponds to the language? Furthermore you could format your code:

It would help people to help you :slight_smile: