Question: How to generate a stripplot like this in Python or R?
2
gravatar for Ting-You Wang
5 months ago by
Hong Kong/The University of Hong Kong
Ting-You Wang80 wrote:

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

enter image description here

Thank you so much in advance.

R rna-seq visualization python • 316 views
ADD COMMENTlink modified 4 months ago by zx87547.9k • written 5 months ago by Ting-You Wang80

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

ADD REPLYlink written 5 months ago by steve2.2k

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).

ADD REPLYlink modified 5 months ago • written 5 months ago by Ting-You Wang80
  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
ADD REPLYlink written 5 months ago by cpad011211k
1

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.

ADD REPLYlink written 5 months ago by Ting-You Wang80

Related post: Plots in R for bioinformatics analyses

ADD REPLYlink written 4 months ago by zx87547.9k
1
gravatar for cpad0112
5 months ago by
cpad011211k
India
cpad011211k wrote:

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")
ADD COMMENTlink written 5 months ago by cpad011211k
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