r - 突出显示 ggplot 堆积条形图中的一个因素

Question

我有几个实验的数据，这些数据给出了我想用堆积条形图表示的样本中物种 DNA 的比例。示例数据是

sample_df <- structure(list(sample = c("R17108_BSSE_QGF_132757_HHWVVDRXX_1_G44937_CCGTGAAG_CAGTGGAT_S29_L001", 
"R17108_BSSE_QGF_132757_HHWVVDRXX_1_G44937_CCGTGAAG_CAGTGGAT_S29_L001", 
"R17108_BSSE_QGF_132757_HHWVVDRXX_1_G44937_CCGTGAAG_CAGTGGAT_S29_L001", 
"R18676", "R18676", "R23399_COW6673A59_S33", "R23399_COW6673A59_S33", 
"R23464_COW5599A32_S33", "R23464_COW5599A32_S33", "R23464_COW5599A32_S33", 
"R24033_concatreseq", "R24033_concatreseq", "R24033_concatreseq", 
"R24033_concatreseq", "R24033_concatreseq", "R24033_concatreseq", 
"R24033_concatreseq", "R24033", "R24033", "R24033", "R24033", 
"R24033", "R24033", "R30216_concatreseq", "R30216_concatreseq", 
"R30216", "R30216", "R31417_concatreseq", "R31417", "R32064", 
"R32064", "R32064", "R32064", "R4752_BSSE_QGF_132888_HHWVVDRXX_1_G45072_CAGGAGCC_GTCCAATC_S159_L001", 
"R4752_BSSE_QGF_132888_HHWVVDRXX_1_G45072_CAGGAGCC_GTCCAATC_S159_L001", 
"R4752_BSSE_QGF_132888_HHWVVDRXX_1_G45072_CAGGAGCC_GTCCAATC_S159_L001", 
"R4752_BSSE_QGF_132888_HHWVVDRXX_1_G45072_CAGGAGCC_GTCCAATC_S159_L001", 
"R4752_BSSE_QGF_132888_HHWVVDRXX_1_G45072_CAGGAGCC_GTCCAATC_S159_L001", 
"R4775_LFO46Pool105_3311__L5_ACCACTGT_L005", "R4775_LFO46Pool105_3311__L5_ACCACTGT_L005"
), name = c("Microbacterium sp. LKL04", "Microbacterium oleivorans", 
"Mycobacterium tuberculosis", "Staphylococcus cohnii", "Mycobacterium tuberculosis", 
"Paraburkholderia fungorum", "Paraburkholderia xenovorans", "Paraburkholderia fungorum", 
"Paraburkholderia aromaticivorans", "Paraburkholderia xenovorans", 
"Bacillus safensis", "Bacillus sp. WP8", "Bacillus sp. PAMC28571", 
"Bacillus sp. PAMC22265", "Bacillus pumilus", "Bacillus altitudinis", 
"Bacillus subtilis", "Bacillus safensis", "Bacillus sp. WP8", 
"Bacillus sp. PAMC28571", "Bacillus sp. PAMC22265", "Bacillus pumilus", 
"Bacillus altitudinis", "Mycobacterium avium", "Mycobacterium tuberculosis", 
"Mycobacterium avium", "Mycobacterium tuberculosis", "Mycobacterium avium", 
"Mycobacterium avium", "Staphylococcus aureus", "Paenibacillus sp. 32O-W", 
"Mycobacterium tuberculosis", "Homo sapiens", "Ralstonia pickettii", 
"Ralstonia mannitolilytica", "Ralstonia insidiosa", "Ralstonia solanacearum", 
"Mycobacterium tuberculosis", "Paenibacillus naphthalenovorans", 
"Paenibacillus sp. B01"), fraction_total_reads = c(0.29347, 0.09071, 
0.46242, 0.6525, 0.32403, 0.92541, 0.01772, 0.8842, 0.04011, 
0.01561, 0.72733, 0.02744, 0.11121, 0.02673, 0.03845, 0.02282, 
0.01176, 0.73674, 0.02711, 0.12122, 0.01858, 0.03677, 0.02115, 
0.97964, 0.01579, 0.98397, 0.01227, 0.9907, 0.99348, 0.43967, 
0.01337, 0.4288, 0.02825, 0.54439, 0.08077, 0.05916, 0.01978, 
0.23135, 0.70247, 0.02424)), row.names = c(NA, -40L), class = c("tbl_df", 
"tbl", "data.frame"))

然后像这样绘制

ggplot(data = sample_df, aes(fill=name, y=fraction_total_reads, x=sample)) + 
    geom_bar(position="stack", stat="identity", color="black") +
    theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))

要得到

问题是我主要对结核分枝杆菌感兴趣，但它的颜色经常在其他分枝杆菌物种中丢失，所以它并不突出。有没有一种方法可以为一个物种分配特定的不同颜色或背景或边界，而不必为所有物种分配颜色？我的真实数据有超过 1000 个物种，所以这将是非常劳动密集型的。在其他地方，我看到它建议我像这样创建一个新列

sample_df2 <- sample_df %>%
    mutate(is_mtb = ifelse(name == "Mycobacterium tuberculosis", TRUE, FALSE))

然后用

ggplot(data = sample_df2, aes(fill=is_mtb, y=fraction_total_reads, x=sample)) + 
    geom_bar(position="stack", stat="identity") +
    theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))

但这丢失了太多信息，因为我看不到其他物种是什么。
如果我有一个像第一个以某种方式突出显示结核分枝杆菌的图，以及每个条形图的底部，那对我来说是最好的。

Answer 1

你可以这样处理它:

library(ggplot2)

# define default colours for each name
mynames <- unique(sample_df$name)
mycolours <- scales::hue_pal()(length(mynames))
mycolours <- setNames(mycolours, mynames)

# set up custom colour!
mycolours["Mycobacterium tuberculosis"] <- "red"

# your plot
ggplot(data = sample_df, aes(fill=name, y=fraction_total_reads, x=sample)) + 
 geom_bar(position="stack", stat="identity", color="black") +
 theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1)) +
 
 # add this! 
 scale_fill_manual(values = mycolours)

你可以用这个更突出它:

library(ggplot2)

mynames <- unique(sample_df$name)

myfills <- scales::hue_pal()(length(mynames))
myfills <- setNames(myfills, mynames)
myfills["Mycobacterium tuberculosis"] <- "red"

mycolours <- rep("black", length(mynames))
mycolours <- setNames(mycolours, mynames)
mycolours["Mycobacterium tuberculosis"] <- "red"

myalphas <- rep(0.6, length(mynames))
myalphas <- setNames(myalphas, mynames)
myalphas["Mycobacterium tuberculosis"] <- 1


ggplot(data = sample_df, aes(y = fraction_total_reads, 
                             x = sample, 
                             alpha  = name,
                             colour = name,
                             fill   = name)) + 
 geom_bar(position = "stack", stat = "identity") +
 theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1)) +
 scale_fill_manual  (values = myfills  ) +
 scale_colour_manual(values = mycolours) +
 scale_alpha_manual (values = myalphas )