使用dplyr在组会议条件中聚合行

Question

我有一张表格，格式如下：

Sample     Location     Phylum           Abundance
1          Teat canal   Firmicutes       0.34
1          Teat canal   Actinobacteria   0.26
1          Teat canal   Candidatus       0.001
1          Teat canal   Chloroflexi      0.001
2          Teat canal   Firmicutes       0.30
2          Teat canal   Actinobacteria   0.24
2          Teat canal   Apicomplexa      0.005
2          Teat canal   Chloroflexi      0.001

我想要(1)计算每个门在每个位置上的平均丰度；(2)将平均丰度小于0.01的门重新命名+级联成一个单独的类别，称为其他类别。首先，我做了以下工作：

phym %>%
  group_by(Location, Phylum) %>%
  summarise(MeanAbundance = mean(Abundance)) %>%
  mutate(Phylum = ifelse(MeanAbundance < 0.01, "Other", levels(Phylum)[Phylum]))

这将计算每个门在每个位置的平均丰度，并重新命名门，其平均丰度小于0.01。如何增强此代码以连接每个位置内的其他类别的丰度值(假设有多个不同的位置)？

Answer 1

一种选择是按“位置”、“叶”进行分组，用mutate创建“mutate”列，然后按“位置”分组，将“MeanAbundance”连接到unique 'Phylum'，其中“MeanAbundance”小于0.01为一个字符串(toSTring)，类似地，转换为“Other”的级别也连接在“Phylum”中。

library(dplyr)
phym %>%
    group_by(Location, Phylum) %>%
    mutate(MeanAbundance = mean(Abundance)) %>%
    group_by(Location) %>%
    summarise(Othergroup = toString(unique(Phylum[MeanAbundance < 0.01])),
            Phylum = toString(unique(ifelse(MeanAbundance < 0.01, 
                  "Other", levels(Phylum)[Phylum]))))
# A tibble: 1 x 3
#Location   Othergroup                           Phylum                           
#   <chr>      <chr>                                <chr>                            
#1 Teat canal Candidatus, Chloroflexi, Apicomplexa Firmicutes, Actinobacteria, Other

数据

phym <- structure(list(Sample = c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L), 
 Location = c("Teat canal", 
"Teat canal", "Teat canal", "Teat canal", "Teat canal", "Teat canal", 
"Teat canal", "Teat canal"), Phylum = structure(c(5L, 1L, 3L, 
4L, 5L, 1L, 2L, 4L), .Label = c("Actinobacteria", "Apicomplexa", 
"Candidatus", "Chloroflexi", "Firmicutes"), class = "factor"), 
    Abundance = c(0.34, 0.26, 0.001, 0.001, 0.3, 0.24, 0.005, 
    0.001)), row.names = c(NA, -8L), class = "data.frame")