我已經撰寫了下面的代碼來創建一個火山圖，該圖基于data.frame“gseaRes”的變數“group”著色。彩色點指的是我感興趣的路徑，其他（不感興趣的）應該是灰色的，在背景中。我在 geom_point 中使用了引數“alpha”來使其更透明，但是彩色點在灰點內部總是模糊不清，灰點幾乎看不到，所以我們失去了它們有多少的資訊。如果某人知道如何在兩層中繪制這些點，我在徘徊，就像我們在頂部使用散點圖和線條一樣。是否有引數或其他編碼方式？
這是我使用的資料集：https ://github.com/mariakondili/GSEA/blob/main/GSEA_dataframe.tsv
這是我制作它的方式：
suppressPackageStartupMessages(library(tidyverse))
gseaRes %>%
mutate("group" = ifelse(str_detect(pathway,"blabla1"),"group1",
ifelse(str_detect(pathway,"blabla2"), "group2",
ifelse(str_detect(pathway,"blabla3"), "group3",
ifelse(str_detect(pathway,"blabla4"), "group4",
ifelse(str_detect(pathway,"blabla5"),"group5","Other"))))))
ggplot(gseaRes , aes(x=-log10(padj), y=NES, size=size, col=group))
geom_point(alpha=ifelse(gseaRes$group=="Other",0.02, 1))
scale_color_manual(values = c("group1" = "violetred",
"group2" = "royalblue1" ,
"group3"="orange",
"group4" = "cyan",
"group5" ="tomato4",
"Other" = "grey30")) theme_classic()
uj5u.com熱心網友回復：
您可以使用兩個geom_point傳遞過濾資料集的物件，一個僅包含“其他”類別，一個包含您感興趣的路徑：
library(tidyverse)
gseaRes <- read_tsv("https://raw.githubusercontent.com/mariakondili/GSEA/main/GSEA_dataframe.tsv")
gseaRes <- gseaRes %>%
mutate(group = ifelse(str_detect(pathway, "_ACTIN"), "group1",
ifelse(str_detect(pathway, "blabla"), "group2",
ifelse(str_detect(pathway, "blabla"), "group3",
ifelse(str_detect(pathway, "blabla"), "group4",
ifelse(str_detect(pathway, "blabla"), "group5", "Other")
)
)
)
))
ggplot(gseaRes, aes(x = -log10(padj), y = NES, size = size, col = group))
geom_point(data = filter(gseaRes, group == "Other"), alpha = .02)
geom_point(data = filter(gseaRes, !group == "Other"))
scale_color_manual(values = c(
"group1" = "violetred",
"group2" = "royalblue1",
"group3" = "orange",
"group4" = "cyan",
"group5" = "tomato4",
"Other" = "grey30"
))
theme_classic()
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標籤：rggplot2散点图
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