散点图中的颜色编码误差条 [英] Color coding error bars in a plotly scatter plot

问题描述

我正在尝试使用 R

这与我想要的非常接近，除了:

1. 我希望误差条的颜色与效果大小相似(通过相应的 p 值).
2. 移除 colorbar
下面的两个 trace 图例
3. y 轴上标签的顺序是否为 factors

有什么想法吗?

解决方案

好吧，我花了一段时间来预热我的 plotly 技能.由于您的第一点是最困难的，所以我将反向通过您的点.

• 3. 这可以通过使用 categoryorder 操作 layout 来实现和 yaxis-list 中的 categoryarray(参见 motos 回答

     代码(颜色条产生了一些问题):

     ### 设置分类顺序yform <- list(categoryorder = "array",categoryarray = rev(因子)，title="因子",zeroline=F,showticklabels=T)### 设置色阶并将其转换为十六进制库(grDevices)mycramp<-colorRamp(c("darkred","gray"))mycolors<-rgb(mycramp(p.values),maxColorValue = 255)### 没有调整颜色条的绘图图书馆(情节)### 没有颜色条调整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)) %>%布局(xaxis=list(title="效果大小",zeroline=T,showticklabels=T),yaxis=yform)###颜色条调整踢出散点的原始颜色.要么你把它们画出来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)) %>%布局(xaxis=list(title="效果大小",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) %>%布局(xaxis=list(title="效果大小",zeroline=T,showticklabels=T),yaxis=yform)### 或者您尝试在绘图之前设置颜色条.这会导致一些警告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)) %>%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 <代码>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:

     1. I'd like the error bars to be colored similar to the effect sizes (by the corresponding p-values).
     2. Remove the two trace legends below the colorbar
     3. 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.

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

     • 2. Set showlegend=FALSE

     • 1. 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.

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