UpSetR基础绘图

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于 2024-01-30 20:15:05 首次发布

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本文介绍了如何在R中利用UpSetR包对基因家族成员数据进行可视化，包括基本绘图、自定义x轴顺序、度量排序、颜色调整和阴影设置等操作。作者通过示例数据展示了如何一步步创建定制的UpSet图。

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加载包

library(RColorBrewer)
library(UpSetR)

示例数据——以列表为例

> listInput
$d1
 [1] "BPEp"      "GBF3"      "SRM1"      "WRKY6"     "ATBZIP53"  "GBF5"      "RGA"       "ATMYB3R5" 
 [9] "BIM1"      "CDF3"      "SPT"       "PIF1"      "bHLHb1"    "AtbZIP16"  "PIF3"      "DPBF1"    
[17] "PCF1"      "bZIP44"    "ATMYB3R-1" "ATBZIP42" 

$d3
 [1] "CDF3"    "BAM8"    "DOF5.6"  "MYB94"   "RGA"     "JKD"     "AtTCP15" "PIF3"    "SPT"     "CIB4"   
[11] "AtTCP14" "BPEp"    "ATMYB73" "PIF1"    "TCP23"   "bHLHb1"  "PIF8"    "PCF1"    "ATMYB60" "ATMYB98"

$d6
 [1] "PCF1"    "OBP3"    "PIF8"    "SPT"     "AGL20"   "CIB4"    "MYB94"   "CDF3"    "WRKY6"   "COG1"   
[11] "DOF5.6"  "NAP"     "BPEp"    "OBP1"    "BIM2"    "NAC047"  "RGA"     "AtTCP15" "BZR1"    "AtTCP14"

$d12
 [1] "GBF3"    "BPEp"    "BW62B"   "RGA"     "TCP23"   "DOF5.6"  "BEH4"    "BZR1"    "AtABF2"  "NAC047" 
[11] "SPT"     "AtTCP15" "bHLHb1"  "PIF8"    "GBF5"    "ATBPC1"  "JKD"     "PCF1"    "CDF3"   

$d24
 [1] "BZR1"     "PCF1"     "bHLHb1"   "PIF8"     "BPEp"     "RGA"      "SPT"      "TCP9"     "GBF5"    
[10] "JKD"      "NAC047"   "bHLH104"  "CDF3"     "MGP"      "BBR/BPC6" "bHLH13"   "DPBF1"    "AtABF2"  
[19] "BAM8"     "AtbZIP16"

基础绘图

upset(fromList(listInput))

在这里插入图片描述

x轴按照指定顺序排列

upset(fromList(listInput), 
      sets=c("d24","d12","d6","d3","d1"),
      keep.order=T)

在这里插入图片描述

x轴按照degree排序

upset(fromList(listInput), 
       sets=c("d24","d12","d6","d3","d1"),
       keep.order=T,order.by = c("degree"))

在这里插入图片描述

upset(fromList(listInput), 
       sets=c("d24","d12","d6","d3","d1"),
       keep.order=T,order.by = c("degree")，
       decreasing = F)

在这里插入图片描述

修改x轴颜色

upset(fromList(listInput), 
      sets=c("d24","d12","d6","d3","d1"),
      keep.order=T,
      order.by = c("degree"),
      decreasing = F,
      sets.bar.color=brewer.pal(5,"YlOrBr"))

在这里插入图片描述

X轴阴影修改颜色

upset(fromList(listInput), 
      sets=c("d24","d12","d6","d3","d1"),
      keep.order=T,
      order.by = c("degree"),
      decreasing = F,
      sets.bar.color=brewer.pal(5,"YlOrBr"),
      shade.color="#4292C6")

在这里插入图片描述