我正在尝试使用 R%add_trace(type='scatter',mode="markers",y=~factors,x=~effect.sizes,color=~p.values,colors=grDevices::colorRamp(c("darkred","gray")),error_x=list(array=effect.errors,color=mycolors),split=factors,showlegend=FALSE,marker=list(color=mycolors)) %>%布局(xaxis=list(title="效果大小",zeroline=T,showticklabels=T),yaxis=yform)

奇怪的是，这第一点是如此难以解决并导致如此大的代码括号，因为通常 plotly 很好地支持该管道逻辑，并且您会得到一个非常可读的代码，其中包含所有 添加-功能.

我希望，例如，一些 add_errorbar-function，但显然你必须在 plot_ly-function 中添加错误栏，并且错误的颜色向量仅在以下情况下才有效您使用 split 功能.如果有人想对此发表评论或发布具有更易读代码的替代答案，那将很有趣.

I'm trying to create a forest plot with R plotly where I want to color code the effect sizes (points) and their error bars by their corresponding p-values.

Here are toy data:

set.seed(1)

factors <- paste0(1:25,":age")
effect.sizes <- rnorm(25,0,1)
effect.errors <- abs(rnorm(25,0,1))
p.values <- runif(25,0,1)

Here's what I'm trying:

library(dplyr)
plotly::plot_ly(type='scatter',mode="markers",y=~factors,x=~effect.sizes,color=~p.values,colors=grDevices::colorRamp(c("darkred","gray"))) %>%
      plotly::add_trace(error_x=list(array=effect.errors),marker=list(color=~p.values,colors=grDevices::colorRamp(c("darkred","gray")))) %>%
      plotly::colorbar(limits=c(0,1),len=0.4,title="P-Value") %>%
      plotly::layout(xaxis=list(title="Effect Size",zeroline=T,showticklabels=T),yaxis=list(title="Factor",zeroline=F,showticklabels=T))

which gives me:

Which is pretty close to what I want except for:

I'd like the error bars to be colored similar to the effect sizes (by the corresponding p-values). Remove the two trace legends below the colorbar Have the order of the labels on the y-axis be that of factors

Any idea?

解决方案

Okay it took me a while to warm up my plotly skills. Since your first point was the most difficult, I will go reversely through your points.

That can be achied by manipulating the layout using categoryorder and categoryarray in the yaxis-list (cf. motos answer here)

Set showlegend=FALSE

That was tricky. I had to move your second line (the error bars) in the first. Added a color vector to it. Put it in the plot_ly-function. Used split to allow the correct coloring by group. Added the color for the points in a marker-list. In additon I converted the p.values via the colorRamp to hex-because every simpler solution didn't work for me.

Looks like this:

The code (the colorbar created some issues):

### Set category order
yform <- list(categoryorder = "array",
              categoryarray = rev(factors),
              title="Factor",zeroline=F,showticklabels=T)

### set the color scale and convert it to hex
library(grDevices)
mycramp<-colorRamp(c("darkred","gray"))
mycolors<-rgb(mycramp(p.values),maxColorValue = 255)

### plot without the adjusted colorbar
library(plotly)
### Without colorbar adjustment
  plot_ly(type='scatter',mode="markers",y=~factors,x=~effect.sizes,
          color=~p.values,colors=grDevices::colorRamp(c("darkred","gray")),
          error_x=list(array=effect.errors,color=mycolors),split=factors,showlegend=FALSE,marker=list(color=mycolors)) %>%
      layout(xaxis=list(title="Effect Size",zeroline=T,showticklabels=T),yaxis=yform)

  ### The colorbar-adjustment kicks out the original colors of the scatter points. Either you plot them over
  plot_ly(type='scatter',mode="markers",y=~factors,x=~effect.sizes,
          color=~p.values,colors=grDevices::colorRamp(c("darkred","gray")),
          error_x=list(array=effect.errors,color=mycolors),split=factors,showlegend=FALSE,marker=list(color=mycolors)) %>%
      layout(xaxis=list(title="Effect Size",zeroline=T,showticklabels=T),yaxis=yform) %>%
  colorbar(limits=c(0,1),len=0.4,title="P-Value",inherit=FALSE) %>%
      add_trace(type='scatter',mode="markers",y=~factors,x=~effect.sizes,
            showlegend=FALSE,marker=list(color=mycolors),inherit=FALSE) %>%
    layout(xaxis=list(title="Effect Size",zeroline=T,showticklabels=T),yaxis=yform)

  ### or you try to set the colorbar before the plot. This results in some warnings
  plot_ly() %>%
  colorbar(limits=c(0,1),len=0.4,title="P-Value",inherit=FALSE) %>%
      add_trace(type='scatter',mode="markers",y=~factors,x=~effect.sizes,
          color=~p.values,colors=grDevices::colorRamp(c("darkred","gray")),
          error_x=list(array=effect.errors,color=mycolors),split=factors,showlegend=FALSE,marker=list(color=mycolors)) %>%
      layout(xaxis=list(title="Effect Size",zeroline=T,showticklabels=T),yaxis=yform)

Just odd that this first point was so difficult to solve and results in such a big code bracket, because normally plotly supports that pipe logic quite well and you get a very readable code with all the add-functions.

I expected e.g., some add_errorbar-function, but apparently you have to add the errorbars in the plot_ly-function and the color-vector for the errors only works if you use the split-function. If someone would like to comment or post an alternative answer with more readable code on this, that would be interesting.