使用R包barplot3d绘制3D条形图-2020-07-04Sat

## 1.设置当前工作目录

setwd("./barplot3d/")

## 2.安装和导入R包

# install.packages("barplot3d")

library(barplot3d)

## 3.R包简介

### 3.1 Description

help(package="barplot3d")

# Package: barplot3d

# Type: Package

# Title: Create 3D Barplots

# Version: 1.0.1

# Authors@R: person("Christopher", "Wardell", email="r@cpwardell.com", role=c("aut","cre"))

# Description: Creates 3D barplots. Includes a function for sequence context plots used in DNA sequencing analysis.

# License: Apache License 2.0 | file LICENSE

# Encoding: UTF-8

# LazyData: true

# Imports: rgl

# RoxygenNote: 6.1.1

# Suggests: knitr, rmarkdown

# VignetteBuilder: knitr

# NeedsCompilation: no

# Packaged: 2019-11-05 03:21:48 UTC; cpw

# Author: Christopher Wardell [aut, cre]

# Maintainer: Christopher Wardell <r@cpwardell.com>

# Repository: CRAN

# Date/Publication: 2019-11-06 15:40:07 UTC

# Built: R 4.0.2; ; 2020-06-27 22:17:10 UTC; windows

### 3.2 Package structure

ls(package:barplot3d)

# [1] "bar3d" "barplot3d" "legoplot3d"

################

## 4.开始测试 ##

################

### 4.1 Two example plots

#### 4.1.1 Something very simple

## Load packages

library(rgl)

## Make a very simple 3D barplot using mostly defaults

?barplot3d

# Adds a 3D bar plot to the current RGL scene

barplot3d(rows=1,cols=5,z=1:5,theta=10,phi=10,alpha = 0.5)

# 参数测试

#@ 参数：alpha透明度调节

barplot3d(rows=1,cols=5,z=1:5,theta=10,phi=10,alpha = 0.9, topcolors = "#078E53")

#@ 参数：topcolors条形图上顶颜色调节

barplot3d(rows=1,cols=5,z=1:5,theta=10,phi=10,alpha = 0.5, topcolors = "#078E53", sidecolors = "#00B2EE")

#@ 参数：linecolors条形图的边线颜色调整

barplot3d(rows=1,cols=5,z=1:5,theta=10,phi=10,alpha = 0.5, topcolors = "#078E53", sidecolors = "#00B2EE", linecolors = "#EE0000")

#@ 参数：theta水平调整3d条形图的角度

barplot3d(rows=1,cols=5,z=1:5,theta=50,phi=10,alpha = 0.5, topcolors = "#078E53", sidecolors = "#00B2EE", linecolors = "#EE0000")

#@ 参数：phi垂直调整3d条形图的角度

barplot3d(rows=1,cols=5,z=1:5,theta=50,phi=50,alpha = 0.5, topcolors = "#078E53", sidecolors = "#00B2EE", linecolors = "#EE0000")

#@ 参数：gridlines决定是否填加条形图的背景网格，T则填加，F则不填加

barplot3d(rows=1,cols=5,z=1:5,theta=50,phi=50,alpha = 0.5, topcolors = "#078E53", sidecolors = "#00B2EE", linecolors = "#EE0000", gridlines = T)

barplot3d(rows=1,cols=5,z=1:5,theta=50,phi=50,alpha = 0.5, topcolors = "#078E53", sidecolors = "#00B2EE", linecolors = "#EE0000", gridlines = F)

#@ 参数：xlabels, Labels for the x axis (must be a vector of names the same length as "cols" parameter).

barplot3d(rows=1,cols=5,z=1:5,theta=50,phi=50,alpha = 0.5, topcolors = "#078E53", sidecolors = "#00B2EE", linecolors = "#EE0000", gridlines = F, xlabels = c("A", "B", "C", "D", "E"))

#@ 参数：ylabels, Labels for the y axis (must be a vector of names the same length as "rows" parameter).

barplot3d(rows=1,cols=5,z=1:5,theta=50,phi=50,alpha = 0.5, topcolors = "#078E53", sidecolors = "#00B2EE", linecolors = "#EE0000", gridlines = F, xlabels = c("A", "B", "C", "D", "E"), ylabels = "value")

#@ 参数：zlabels, Labels for the z axis; add numeric scale to the vertical dimension of the plot (TRUE or FALSE).

#@ 参数：xsub

barplot3d(rows=1,cols=5,z=1:5,theta=60,phi=10,alpha = 0.5, topcolors = "#078E53", sidecolors = "#00B2EE", linecolors = "#EE0000", gridlines = F, xlabels = c("A", "B", "C", "D", "E"), ylabels = "value", zlabels = T, xsub = "Samples")

#@ 参数：ysub

#@ 参数：zsub

#### 4.1.2 Something more decorative

## Make a prettier 3D barplot with more advanced features

inputdata=round(rnorm(15,10,3))

barplot3d(rows=3,cols=5,z=inputdata,scalexy=5,alpha=0.4,theta=30,phi=50,

topcolors=rainbow(15),xlabels = 1:5,ylabels=LETTERS[1:3],

xsub="Numbers",ysub="Letters",zsub="Count")

#@ 重新构建一个更庞大的3d条形图

big_inputdata <- round(rnorm(100, 50, 2))

barplot3d(rows=10,cols=10,z=big_inputdata,scalexy=5,alpha=0.4,theta=30,phi=50, topcolors=rainbow(100),xlabels = 1:10,ylabels=LETTERS[1:10], xsub="Numbers",ysub="Letters",zsub="Count")

### 4.3 Viewing angles, plot size and saving your plot

# “theta” rotates the viewpoint in the horizontal plane (imagine it on a rotating turntable) and can be set between 0 and 360 degrees.

# “phi” rotates the viewpoint in the vertical plane (imagine going below and above the plot) and can be set between -90 to 90 (-90 is directly below, 90 directly above).

# The 4 arguments are the position (in pixels) of the left, top, right and bottom edges of the rgl viewing window

# This code leads to a plot that is 600 pixels wide and 400 pixels tall.

par3d(windowRect=c(0,50,600,450))

# Save the current rgl view

rgl.snapshot("filename.png")

# Error in rgl.snapshot("filename.png") :

# pixmap save format not supported in this build

### 4.4 Legoplots

# Read in COSMIC signature probabilities

x=system.file("extdata", "signature_probabilities.txt", package = "barplot3d")

sigdata=read.table(x,header=TRUE,stringsAsFactors = FALSE)

# Plot signature 2 without axis labels, with Sanger colors and some transparency so we can see all bars

legoplot3d(contextdata=sigdata$Signature_2,labels=FALSE,scalexy=0.05,sixcolors="sanger",alpha=0.4)

# Plot signature 2 without axis labels, with Sanger colors and some transparency so we can see all bars

legoplot3d(contextdata=sigdata$Signature_8,labels=FALSE,scalexy=0.01,sixcolors="broad",alpha=0.4)

# Input data MUST be in this order

cat(sigdata$Somatic_mutation_type,sep="\n")

# C>A|G>T_AxA

# C>A|G>T_CxA

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## 5.测试完成

sessionInfo()

# R version 3.6.3 (2020-02-29)

# Platform: x86_64-w64-mingw32/x64 (64-bit)

# Running under: Windows 10 x64 (build 18363)

# Matrix products: default

# locale:

# [1] LC_COLLATE=Chinese (Simplified)_China.936

# [2] LC_CTYPE=Chinese (Simplified)_China.936

# [3] LC_MONETARY=Chinese (Simplified)_China.936

# [4] LC_NUMERIC=C

# [5] LC_TIME=Chinese (Simplified)_China.936

# attached base packages:

# [1] stats graphics grDevices utils datasets methods

# [7] base

# other attached packages:

# [1] rgl_0.100.54 barplot3d_1.0.1

# loaded via a namespace (and not attached):

# [1] Rcpp_1.0.4.6 packrat_0.5.0

# [3] digest_0.6.25 later_1.1.0.1

# [5] mime_0.9 R6_2.4.1

# [7] xtable_1.8-4 jsonlite_1.7.0

# [9] magrittr_1.5 rlang_0.4.6

# [11] miniUI_0.1.1.1 promises_1.1.1

# [13] webshot_0.5.2 tools_3.6.3

# [15] manipulateWidget_0.10.1 htmlwidgets_1.5.1

# [17] crosstalk_1.1.0.1 shiny_1.5.0

# [19] fastmap_1.0.1 httpuv_1.5.4

# [21] xfun_0.15 compiler_3.6.3

# [23] htmltools_0.5.0 knitr_1.29

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