英文:
How to replace NA values in dataframe with adjacent columns value + additional text to differentiate them in R
问题
我好奇是否可以用左侧列中的文本（不是NA值的列）替换数据框中的NA值，然后在末尾添加"_unclassified"文本。
以下是一个示例数据框：
feature <- c("1","2","3","4","5" )phylum <- c("Firmicutes","Firmicutes","Firmicutes","Proteobacteria","Firmicutes" )class <- c(NA,"Clostridia","Clostridia","Gammaproteobacteria","Bacilli" )order <- c(NA,NA,"Oscillospirales","Enterobacterales","Staphylococcales" )family <- c(NA,NA,NA,"Enterobacteriaceae","Staphylococcaceae" )genus <- c(NA,NA,NA,NA,"Staphylococcus")df <- data.frame(feature, phylum, class, order, family, genus)
例如，
feature 1 将在class，order，family，genus中有Firmicutes_unclassified
feature 2 将在order，family和genus中有Clostridia_unclassified
feature 3 将在family和genus中有Oscillospirales_unclassified
feature 4 将在genus中有Enterobacteriaceae_unclassified。
英文:
I'm curious if I could replace NA values in my data frame with text from the column to the left (that does not have NA), with an additional "_unclassified" text on the end.
Here is an example data frame:
feature <- c("1","2","3","4","5" )phylum <- c("Firmicutes","Firmicutes","Firmicutes","Proteobacteria","Firmicutes" )class <- c(NA,"Clostridia","Clostridia","Gammaproteobacteria","Bacilli" )order <- c(NA,NA,"Oscillospirales","Enterobacterales","Staphylococcales" )family <- c(NA,NA,NA,"Enterobacteriaceae","Staphylococcaceae" )genus <- c(NA,NA,NA,NA,"Staphylococcus")df <- data.frame(feature, phylum, class, order, family, genus)
For example,
feature 1 would have Firmicutes_unclassified across class, order, family, genus
feature 2 would have Clostridia_unclassified across order, family, and genus
feature 3 would have Oscillospirales_unclassified across family and genus
feature 4 would have Enterobacteriaceae_unclassified for genus
答案1
得分: 1
> dffeature phylum class order family1 1 厚壁菌门 厚壁菌门_未分类 厚壁菌门_未分类 厚壁菌门_未分类2 2 厚壁菌门 梭菌纲 梭菌纲_未分类 梭菌纲_未分类3 3 厚壁菌门 梭菌纲 压摩纲 压摩纲_未分类4 4 变形菌门 伽马变形菌纲 肠杆菌目 肠杆菌科5 5 厚壁菌门 乳杆菌纲 葡萄球菌目 葡萄球菌科genus1 厚壁菌门_未分类2 梭菌纲_未分类3 压摩纲_未分类4 肠杆菌科_未分类5 葡萄球菌
英文:
An option with na.locf from zoo
library(zoo)df[-1] <- t(apply(df[-1], 1, \(x) ifelse(is.na(x), paste0(na.locf0(x),'_unclassified'), x)))
-output
> dffeature phylum class order family1 1 Firmicutes Firmicutes_unclassified Firmicutes_unclassified Firmicutes_unclassified2 2 Firmicutes Clostridia Clostridia_unclassified Clostridia_unclassified3 3 Firmicutes Clostridia Oscillospirales Oscillospirales_unclassified4 4 Proteobacteria Gammaproteobacteria Enterobacterales Enterobacteriaceae5 5 Firmicutes Bacilli Staphylococcales Staphylococcaceaegenus1 Firmicutes_unclassified2 Clostridia_unclassified3 Oscillospirales_unclassified4 Enterobacteriaceae_unclassified5 Staphylococcus
答案2
得分: 1
使用纯粹的基础R，可以使用以下一行代码来执行这个操作：
df[-1] <- t(apply(df[-1], MARGIN=1, function(x) replace(x, is.na(x), paste0(tail(na.omit(x), n=1), '_unclassified'))))df
这行代码会在数据框中去除第一列(df[-1])后，对每一行应用一个匿名函数，该函数会将包含NA值的元素替换为去除NA值后的最后一个元素，并在其后添加 '_unclassified' 后缀。
英文:
One-liner, using just base R.
df[-1] <- t(apply(df[-1], MARGIN=1, \(x) replace(x, is.na(x), paste0(tail(na.omit(x), n=1), '_unclassified'))))df# feature phylum class order family genus# 1 1 Firmicutes Firmicutes_unclassified Firmicutes_unclassified Firmicutes_unclassified Firmicutes_unclassified# 2 2 Firmicutes Clostridia Clostridia_unclassified Clostridia_unclassified Clostridia_unclassified# 3 3 Firmicutes Clostridia Oscillospirales Oscillospirales_unclassified Oscillospirales_unclassified# 4 4 Proteobacteria Gammaproteobacteria Enterobacterales Enterobacteriaceae Enterobacteriaceae_unclassified# 5 5 Firmicutes Bacilli Staphylococcales Staphylococcaceae Staphylococcus
Explanation:
We apply an anonymous function \(x) on MARGIN=1 (i.e. row-wise) on the data frame while excluding first column df[-1]. In the anonymous function we replace in every row x where is.na(x) is TRUE by the tail of length n=1 of na.omit(x) (i.e. x without the NAs while paste0ing suffix '_unclassified' to it.
答案3
得分: 0
以下是翻译好的部分：
library(tidyverse)library(vctrs)feature <- c("1", "2", "3", "4", "5" )phylum <- c("Firmicutes", "Firmicutes", "Firmicutes", "Proteobacteria", "Firmicutes" )class <- c(NA, "Clostridia", "Clostridia", "Gammaproteobacteria", "Bacilli" )order <- c(NA, NA, "Oscillospirales", "Enterobacterales", "Staphylococcales" )family <- c(NA, NA, NA, "Enterobacteriaceae", "Staphylococcaceae")genus <- c(NA, NA, NA, NA, "Staphylococcus")df <- data.frame(feature, phylum, class, order, family, genus)df2 <- df %>%t() %>%as_tibble(.name_repair = ~vec_as_names(..., repair = "unique", quiet = TRUE)) %>%mutate(across(everything(), ~if_else(is.na(.x),paste0(vec_fill_missing(.x, direction = "down"), "_unclassified"),.x))) %>%t() %>%as_tibble(.name_repair = ~colnames(df))df2#> # A tibble: 5 × 6#> feature phylum class order family genus#> <chr> <chr> <chr> <chr> <chr> <chr>#> 1 1 Firmicutes Firmicutes_unclassified Firmicutes_unclas… Firmi… Firm…#> 2 2 Firmicutes Clostridia Clostridia_unclas… Clost… Clos…#> 3 3 Firmicutes Clostridia Oscillospirales Oscil… Osci…#> 4 4 Proteobacteria Gammaproteobacteria Enterobacterales Enter… Ente…#> 5 5 Firmicutes Bacilli Staphylococcales Staph… Stap…
创建于2023年02月10日，使用 reprex v2.0.2
英文:
Here is one potential solution which transposes the dataframe, fills the NAs with the most recent non-NA value, then transposes the dataframe back again:
library(tidyverse)library(vctrs)feature <- c("1", "2", "3", "4", "5" )phylum <- c("Firmicutes", "Firmicutes", "Firmicutes", "Proteobacteria", "Firmicutes" )class <- c(NA, "Clostridia", "Clostridia", "Gammaproteobacteria", "Bacilli" )order <- c(NA, NA, "Oscillospirales", "Enterobacterales", "Staphylococcales" )family <- c(NA, NA, NA, "Enterobacteriaceae", "Staphylococcaceae")genus <- c(NA, NA, NA, NA, "Staphylococcus")df <- data.frame(feature, phylum, class, order, family, genus)df2 <- df %>%t() %>%as_tibble(.name_repair = ~vec_as_names(..., repair = "unique", quiet = TRUE)) %>%mutate(across(everything(), ~if_else(is.na(.x),paste0(vec_fill_missing(.x, direction = "down"), "_unclassified"),.x))) %>%t() %>%as_tibble(.name_repair = ~colnames(df))df2#> # A tibble: 5 × 6#> feature phylum class order family genus#> <chr> <chr> <chr> <chr> <chr> <chr>#> 1 1 Firmicutes Firmicutes_unclassified Firmicutes_unclas… Firmi… Firm…#> 2 2 Firmicutes Clostridia Clostridia_unclas… Clost… Clos…#> 3 3 Firmicutes Clostridia Oscillospirales Oscil… Osci…#> 4 4 Proteobacteria Gammaproteobacteria Enterobacterales Enter… Ente…#> 5 5 Firmicutes Bacilli Staphylococcales Staph… Stap…
<sup>Created on 2023-02-10 with reprex v2.0.2</sup>
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