交互可视化plotly之3D plot

生信编程日常

发布于 2020-04-01 16:22:04

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发布于 2020-04-01 16:22:04

文章被收录于专栏：生物信息学、python、R、linux生物信息学、python、R、linux

library(plotly)
mtcars$am[which(mtcars$am == 0)] <- 'Automatic'
mtcars$am[which(mtcars$am == 1)] <- 'Manual'
mtcars$am <- as.factor(mtcars$am)
head(mtcars)

分别以wt，hp,qsec为xyz轴作图 add_markers(p, x = NULL, y = NULL, z = NULL, …, data = NULL, inherit = TRUE)

p： a plotly object
data： A data frame (optional) or SharedData object.
inherit： inherit attributes from plot_ly()?
x： the x variable.
y： the y variable.
z： a numeric matrix

基础的3D scatter plot

fig <- plot_ly(mtcars, x = ~wt, y = ~hp, z = ~qsec, color = ~am, colors = c('#BF382A', '#0C4B8E'))
fig <- fig %>% add_markers()
fig <- fig %>% layout(scene = list(xaxis = list(title = 'Weight'),
                     yaxis = list(title = 'Gross horsepower'),
                     zaxis = list(title = '1/4 mile time')))

fig

3D scatter plot添加颜色范围

fig <- plot_ly(mtcars, x = ~wt, y = ~hp, z = ~qsec,
               marker = list(color = ~mpg, colorscale = c('#FFE1A1', '#683531'), showscale = TRUE))
fig <- fig %>% add_markers()
fig <- fig %>% layout(scene = list(xaxis = list(title = 'Weight'),
                                   yaxis = list(title = 'Gross horsepower'),
                                   zaxis = list(title = '1/4 mile time')),
                      annotations = list(
                        x = 1.13,
                        y = 1.05,
                        text = 'Miles/(US) gallon',
                        xref = 'paper',
                        yref = 'paper',
                        showarrow = FALSE
                        ))
fig

3D气泡图

data <- read.csv("https://raw.githubusercontent.com/plotly/datasets/master/gapminderDataFiveYear.csv")

data_2007 <- data[which(data$year == 2007),]
data_2007 <- data_2007[order(data_2007$continent, data_2007$country),]
data_2007$size <- data_2007$pop
colors <- c('#4AC6B7', '#1972A4', '#965F8A', '#FF7070', '#C61951')

fig <- plot_ly(data_2007, x = ~gdpPercap, y = ~lifeExp, z = ~pop, color = ~continent, size = ~size, colors = colors,
             marker = list(symbol = 'circle', sizemode = 'diameter'), sizes = c(5, 150),
             text = ~paste('Country:', country, '<br>Life Expectancy:', lifeExp, '<br>GDP:', gdpPercap,
                           '<br>Pop.:', pop))
fig <- fig %>% layout(title = 'Life Expectancy v. Per Capita GDP, 2007',
         scene = list(xaxis = list(title = 'GDP per capita (2000 dollars)',
                      gridcolor = 'rgb(255, 255, 255)',
                      range = c(2.003297660701705, 5.191505530708712),
                      type = 'log',
                      zerolinewidth = 1,
                      ticklen = 5,
                      gridwidth = 2),
               yaxis = list(title = 'Life Expectancy (years)',
                      gridcolor = 'rgb(255, 255, 255)',
                      range = c(36.12621671352166, 91.72921793264332),
                      zerolinewidth = 1,
                      ticklen = 5,
                      gridwith = 2),
               zaxis = list(title = 'Population',
                            gridcolor = 'rgb(255, 255, 255)',
                            type = 'log',
                            zerolinewidth = 1,
                            ticklen = 5,
                            gridwith = 2)),
         paper_bgcolor = 'rgb(243, 243, 243)',
         plot_bgcolor = 'rgb(243, 243, 243)')

fig