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How to generate a stripplot like this in Python or R?

How to generate a stripplot like this in Python or R?

enter image description here

Thank you so much in advance.

rna-seq visualization python r
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updated by zx8754 zx8754 • written by Ting-You Wang Ting-You Wang

in R you can just make a scatter plot in something like ggplot2. You could use facets per gene.

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written by steve steve

enter image description here

Another example is here. I don't think the author used facet to draw this. It seems that it used a special version of jitter (ordered).

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written by Ting-You Wang Ting-You Wang
  1. do a box plot and jitter.
  2. Do not draw box plot boundaries and let median line be there.
  3. Do facet (or equivalent with mfrow) per gene
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written by cpad0112 cpad0112

usually, jitter in boxplot only generates some noise in x-axis to avoid overlapping. I don't know how to do it in an ordered manner. Can you show some code snippet? Thank you.

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written by Ting-You Wang Ting-You Wang

1 answer

some thing like this ?

Rplot

codeL

library(dplyr)
library(tidyr)
df=data.frame(s1=rnorm(1000,0,10), s2=rnorm(1000,1,10), s3=rnorm(1000,2,10))
library(ggplot2)
df1=gather(df,"sample","value")

ggplot(df1, aes(x = sample, y = value)) +
  geom_point(aes(color=sample)) +
  stat_summary(
    fun.y = median,
    fun.ymin = median,
    fun.ymax = median,
    geom = "crossbar",
    color = "red",
    width=0.2,
    linetype = "dotted"
  )+
  ylim(-100,100)+
  theme_bw()+
  theme(legend.position="none")
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written by cpad0112 cpad0112

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