r - 在 R 中使用 openxlsx 进行条件格式化的 Tidyverse/更快的解决方案？

Question

我正在处理看起来像这张表但更大的遗传数据:

ID allele.a allele.b
A      115       90
A      115       90
A      116       90
B      120       82
B      120       82
B      120      82M

我的目标是针对每个 ID 突出显示哪些等位基因与每个 ID 组第一行列出的等位基因不匹配。我需要将数据导出到格式良好的 excel 文件中。

这就是我想要的:



我可以使用以下脚本到达那里，但实际脚本涉及大约 67 个“ID”、1000 行数据和 37 列。运行大约需要 5 分钟，所以我希望找到一个可以显着减少处理时间的解决方案。也许是来自 tidyverse 的“做”解决方案——不知道会是什么样子。

这是我的脚本，包括一个测试 data.frame。还包括一个更大的测试数据框架，用于速度测试。

library(xlsx)
library(openxlsx)
library(tidyverse)

# Small data.frame
dframe <- data.frame(ID = c("A", "A", "A", "B", "B", "B"),
                     allele.a = c("115", "115", "116", "120", "120", "120"),
                     allele.b = c("90", "90", "90", "82", "82", "82M"),
                     stringsAsFactors = F)

# Bigger data.frame for speed test
# dframe <- data.frame(ID = rep(letters, each = 30),
#                      allele.a = rep(as.character(round(rnorm(n = 30, mean = 100, sd = 0.3), 0)), 26),
#                      allele.b = rep(as.character(round(rnorm(n = 30, mean = 90, sd = 0.3), 0)), 26),
#                      allele.c = rep(as.character(round(rnorm(n = 30, mean = 80, sd = 0.3), 0)), 26),
#                      allele.d = rep(as.character(round(rnorm(n = 30, mean = 70, sd = 0.3), 0)), 26),
#                      allele.e = rep(as.character(round(rnorm(n = 30, mean = 60, sd = 0.3), 0)), 26),
#                      allele.f = rep(as.character(round(rnorm(n = 30, mean = 50, sd = 0.3), 0)), 26),
#                      allele.g = rep(as.character(round(rnorm(n = 30, mean = 40, sd = 0.3), 0)), 26),
#                      allele.h = rep(as.character(round(rnorm(n = 30, mean = 30, sd = 0.3), 0)), 26),
#                      allele.i = rep(as.character(round(rnorm(n = 30, mean = 20, sd = 0.3), 0)), 26),
#                      allele.j = rep(as.character(round(rnorm(n = 30, mean = 10, sd = 0.3), 0)), 26),
#                      stringsAsFactors = F)



# Create a new excel workbook ----
wb <- createWorkbook()

# Add a worksheets
addWorksheet(wb, sheet = 1, gridLines = TRUE)

# add the data to the worksheet        
writeData(wb, sheet = 1, dframe, rowNames = FALSE)      

# Create a style to show alleles that do not match the first row.
style_Red_NoMatch <- createStyle(fontColour = "#FFFFFF", # white text
                                 bgFill = "#CC0000", # Dark red background
                                 textDecoration = c("BOLD")) # bold text

Groups <- unique(dframe$ID)

start_time <- Sys.time()
# For each unique group, 
for(i in 1:length(Groups)){

  # Print a message telling us where the script is processing in the file.
  print(paste("Formatting unique group ", i, "/", length(Groups), sep = ""))

  # What are the allele values of the *first* individual in the group?
  Allele.values <- dframe %>% 
    filter(ID == Groups[i]) %>% 
    slice(1) %>% 
    select(2:ncol(dframe)) %>% 
    as.character()

  # for each column that has allele values in it,
  for (j in 1:length(Allele.values)){
    # format the rest of the rows so that a value that does not match the first value gets red style


    conditionalFormatting(wb, sheet = 1, 
                          style_Red_NoMatch, 
                          rows = (which(dframe$ID == Groups[i]) + 1), 
                          cols = 1+j,  rule=paste("<>\"", Allele.values[j], "\"", sep = ""))
  }

}
end_time <- Sys.time()
end_time - start_time

saveWorkbook(wb, "Example.xlsx", overwrite = TRUE)

Answer 1

我想改进的一种方法是申请 conditionalFormatting在整个列上，而不必遍历每个单元格。
这是一种方法。这种方法的一个缺点是它创建了 TRUE 的逻辑向量。和 FALSE用于conditionalFormatting .可以使用 setColWidths 隐藏这些列功能。
资料

library(openxlsx)

 dframe <- data.frame(ID = rep(letters, each = 30),
                      allele.a = rep(as.character(round(rnorm(n = 30, mean = 100, sd = 0.3), 0)), 26),
                      allele.b = rep(as.character(round(rnorm(n = 30, mean = 90, sd = 0.3), 0)), 26),
                      allele.c = rep(as.character(round(rnorm(n = 30, mean = 80, sd = 0.3), 0)), 26),
                      allele.d = rep(as.character(round(rnorm(n = 30, mean = 70, sd = 0.3), 0)), 26),
                      allele.e = rep(as.character(round(rnorm(n = 30, mean = 60, sd = 0.3), 0)), 26),
                      allele.f = rep(as.character(round(rnorm(n = 30, mean = 50, sd = 0.3), 0)), 26),
                      allele.g = rep(as.character(round(rnorm(n = 30, mean = 40, sd = 0.3), 0)), 26),
                      allele.h = rep(as.character(round(rnorm(n = 30, mean = 30, sd = 0.3), 0)), 26),
                      allele.i = rep(as.character(round(rnorm(n = 30, mean = 20, sd = 0.3), 0)), 26),
                      allele.j = rep(as.character(round(rnorm(n = 30, mean = 10, sd = 0.3), 0)), 26),
                      stringsAsFactors = F)

脚本的第一部分没有改变。

# Create a new excel workbook ----
wb <- createWorkbook()

# Add a worksheets
addWorksheet(wb, sheet = 1, gridLines = TRUE)
    
# Create a style to show alleles that do not match the first row.
style_Red_NoMatch <- createStyle(fontColour = "#FFFFFF", # white text
                                 bgFill = "#CC0000", # Dark red background
                                 textDecoration = c("BOLD")) # bold text

然后识别每个 ID 的第一行并合并到原始数据集中。然后检查任何单元格中是否有任何变化(循环通过每一列)。

# selects first row for each ID which will be used as benchmark
first_row <- dframe[!duplicated(dframe$ID), ]

# Creating new df with the first_row columns added
dframe_chk <- merge(dframe, first_row, by = "ID",  all.x = TRUE, suffixes = c("", "_first"))

# Adding TRUE/FALSE factor for each column to see if it matches or not (-1 to exclude ID column)
for (j in names(dframe)[-1]) {
  
  dframe_chk[, paste0(j, "_chk")] <- dframe_chk[, j] == dframe_chk[, paste0(j, "_first")]
  
}

# Remove _first columns when exporting into Excel
cols <- names(dframe_chk)[!grepl("_first", names(dframe_chk))]

# add the data to the worksheet        
writeData(wb, sheet = 1, dframe_chk[, cols], rowNames = FALSE)      

# This is for conditional Formatting
# first_row is header
row_start <- 2

# Need to add 1 to cover full range (as first row is header)
row_end <- nrow(dframe) + 1

# first column is ID
col_start <- 2 

# last column as per the original dataset
col_end <- ncol(dframe)

# this is to point to the _chk column.
# Note if you have columns more than A-Z then this needs to be adjusted
rule_col <- LETTERS[col_end + 1] 

# Using the _chk column to apply conditional formula
conditionalFormatting(wb, sheet = 1, 
                      style_Red_NoMatch, 
                      rows = row_start:row_end,
                      cols = col_start:col_end,  
                      rule = paste0(rule_col, "2 = FALSE"))

# Exported file includes _chk columns. Hide these columns.
setColWidths(wb, sheet = 1, cols = (col_end + 1):length(cols), hidden = TRUE)

saveWorkbook(wb, "Example2.xlsx", overwrite = TRUE)