专栏名称: EasyCharts

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R语言可视化学习笔记之基因组数据可视化

EasyCharts · 公众号 · 前端 · 2017-06-26 10:19

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compare_means(c(GATA3, PTEN, XBP1)~dataset, data = expr)

可以通过select以及remove来决定比较那几个类型，比如这里我们只比较BRCA和OV

ggboxplot(expr, x="dataset", y="GATA3", title = "GATA3", ylab = "Expression", 
color = "dataset", palette = "jco", select = c("BRCA", "OV"))#通过select选择

ggboxplot(expr, x="dataset", y="GATA3", title = "GATA3", ylab = "Expression", 
color = "dataset", palette = "jco", remove = "BRCA")#通过remove选择

通过order来改变各类型在x轴上的顺序

ggboxplot(expr, x="dataset", y="GATA3", title = "GATA3", ylab = "Expression", 
color = "dataset", palette = "jco", order = c("LUSC", "OV", "BRCA"))

通过rotate=TRUE来变换坐标轴

ggboxplot(expr, x="dataset", y="GATA3", title = "GATA3", ylab = "Expression", 
color = "dataset", palette = "jco", rotate=TRUE)

通过combine=TRUE来进行分面（类似于facet）

ggboxplot(expr, x="dataset", y=c("GATA3", "PTEN", "XBP1"), ylab = "Expression", 
color = "dataset", palette = "jco", combine = TRUE)

通过merge=TRUE或者merge=“axis”将三个类型的plot绘制在一个panel中

ggboxplot(expr, x="dataset", y=c("GATA3", "PTEN", "XBP1"), ylab = "Expression",
color = "dataset", palette = "jco", merge = TRUE)

通过merge=flip利用不同癌症类型进行group

ggboxplot(expr, x="dataset", y=c("GATA3", "PTEN", "XBP1"), 
ylab = "Expression", palette = "jco", merge = "flip")

通过add=jitter增加抖动点

ggboxplot(expr, x="dataset", y=c("GATA3", "PTEN", "XBP1"), combine = TRUE,
color = "dataset", palette = "jco", ylab = "Expression", add = "jitter", 
add.params = list(size=0.1, jitter=0.2))

通过add=dotplot增加dotplot

ggboxplot(expr, x="dataset", y=c("GATA3", "PTEN", "XBP1"), 
combine = TRUE, color = "dataset", palette = "jco", ylab = "Expression", 
add = "dotplot", add.params = list(binwidth=0.1, dotsize=0.2))

很多时候我们很像知道箱线图两端的数据，我们可以通过label来进行展示

ggboxplot(expr, x="dataset", y=c("GATA3", "PTEN", "XBP1"), combine = TRUE,
color = "dataset", palette = "jco", ylab = "Expression", add = "jitter", 
add.params = list(size=0.1, jitter=0.2), label = "bcr_patient_barcode", 
label.select = list(top.up=2, top.down=2), 
font.label = list(size=9, face="italic"), repel = TRUE)

2、小提琴图