Box plot and genetic data

Question: Box plot and genetic data

13 days ago by

L_LANKA • 0 wrote:

Hi! I have a question about box plot and data. I made the correlation analysis Spearman. I see a positive connection between gene and phenotypic expression. For example, I have gene AAAA where 1 and 3 - homozygous and 2- heterozygote. I have information about temperature and I make graduation this information from 1 to 8 (1- 36.0-36.5; 2- 36.6 - 37.0 etc). Can I see how genotype correlation with phenotype in box plot graphic? (For example, if a patient has genotype 2 (C\T) so he\she can has temperature from 4 to 6). enter image description here

R gene • 135 views

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modified 12 days ago by Hamid Ghaedi • 570 • written 13 days ago by L_LANKA • 0

Can you edit your post and include some example data? It's difficult to help without more specific information.

ADD REPLY • link written 13 days ago by rpolicastro • 2.0k

Ok, no problem! :) I made a table and a temperature encryption key.

ADD REPLY • link written 13 days ago by L_LANKA • 0

12 days ago by

rpolicastro • 2.0k

rpolicastro • 2.0k wrote:

Some example data.

df <- data.frame(
  patient=sprintf("C%s", seq_len(10)),
  genotype=sample(seq_len(3), 10, replace=TRUE),
  temperature=sample(seq_len(7), 10, replace=TRUE)
)

> head(df, 5)
  patient genotype temperature
1      C1        1           4
2      C2        3           1
3      C3        1           3
4      C4        2           2
5      C5        1           6

A boxplot using ggplot2.

library("tidyverse")

df %>%
  mutate(genotype=as_factor(genotype)) %>%
  ggplot(aes(x=genotype, y=temperature)) +
    geom_boxplot()

enter image description here

Or a stacked barplot as Hamid Ghaedi correctly pointed out.

df %>%
  mutate(across(!patient, as_factor)) %>%
  ggplot(aes(x=genotype, fill=temperature)) +
    geom_bar(position="fill") +
    scale_fill_viridis_d()

enter image description here

ADD COMMENT • link modified 12 days ago • written 12 days ago by rpolicastro • 2.0k

12 days ago by

Hamid Ghaedi • 570

Canada

Hamid Ghaedi • 570 wrote:

Important notice: Box-plot is usually use to show how a quantitative variable is distributed. Especially it does a great job when diffrneces in variance is significant between the groups and you expect to have some outliers ( Like gene expression data). Since you have discretized the tempreature data, using a box-plot for visualization does not make sense anymore, however, you can plot your original tempreature data as box-plot.

Now you have frequency data of tempreature per genotype, you can viusalize the data using a barplot (or prefreably stacked barplot).

ADD COMMENT • link modified 12 days ago • written 12 days ago by Hamid Ghaedi • 570

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