help with error bars

tidyverse
1

Hi everyone, I am new to R and need help adding error bars to my graphs.
my data set is:
Values Conc Media Toxin Genotype
|1|4878.833|250nM|Physio|DMSO|WT|
|2|4884.833|250nM|Physio|DMSO|KO|
|3|4854.167|250nM|OxPhos|DMSO|WT|
|4|4526.833|250nM|OxPhos|DMSO|KO|
|5|4943.500|250nM|Physio|Rotenone|WT|
|6|5108.167|250nM|Physio|Rotenone|KO|
|7|4404.833|250nM|OxPhos|Rotenone|WT|
|8|4970.833|250nM|OxPhos|Rotenone|KO|
|9|2558.167|500nM|Physio|DMSO|WT|
|10|2776.833|500nM|Physio|DMSO|KO|
|11|2906.500|500nM|OxPhos|DMSO|WT|
|12|2319.667|500nM|OxPhos|DMSO|KO|
|13|2446.167|500nM|Physio|Rotenone|WT|
|14|3772.667|500nM|Physio|Rotenone|KO|
|15|3505.667|500nM|OxPhos|Rotenone|WT|
|16|2749.167|500nM|OxPhos|Rotenone|KO|

What I used to create the graphs:

load packages

library(ggplot2)
library(ggpubr)

Import Data

Rename variable (sets "deadcell" to "df")

df <- deadcell

Set all categories to "factors"

df$Conc <- as.factor(df$Conc)
df$Media <- as.factor(df$Media)
df$Toxin <- as.factor(df$Toxin)
df$Genotype <- as.factor(df$Genotype)

Create a ggplot "object"

bp <- ggplot(df, aes(x = Conc, y = Values, group = Media, color = Genotype)) +
geom_point(aes(fill = Genotype, shape = Genotype), size = 2.5)

Creates the plot

bp + facet_wrap(Media~Toxin) +
theme(strip.text.x = element_text(face = "bold"),
axis.title.x = element_text(face = "bold"),
axis.title.y = element_text(face = "bold")) +
labs(x = "\nConcentration", y = "Values\n") + theme_bw()

What my graphs look like. I just need to add error bars. Any help I would appreciate.

f25c34d5-1c6c-420a-9c3c-b59dc8ae88a2
f25c34d5-1c6c-420a-9c3c-b59dc8ae88a2469×400 14.5 KB

2

What do you want the error bars to represent? You have 16 rows of data and you are plotting 16 points. I do not see an obvious basis for error bars.

3

SD, I have another column with their SD, I just need the proper command to to incorporate into this graph. Each point will have its own SD. Thanks!

4

I added an SD column with invented values. The following shows the simplest implementation of error bar.

library(ggplot2)
df <- read.csv("~/R/Play/Dummy1.csv",sep = "|")
df
#>      Values  Conc  Media    Toxin Genotype  SD
#> 1  4878.833 250nM Physio     DMSO       WT 200
#> 2  4884.833 250nM Physio     DMSO       KO 200
#> 3  4854.167 250nM OxPhos     DMSO       WT 200
#> 4  4526.833 250nM OxPhos     DMSO       KO 200
#> 5  4943.500 250nM Physio Rotenone       WT 200
#> 6  5108.167 250nM Physio Rotenone       KO 200
#> 7  4404.833 250nM OxPhos Rotenone       WT 200
#> 8  4970.833 250nM OxPhos Rotenone       KO 200
#> 9  2558.167 500nM Physio     DMSO       WT 250
#> 10 2776.833 500nM Physio     DMSO       KO 250
#> 11 2906.500 500nM OxPhos     DMSO       WT 250
#> 12 2319.667 500nM OxPhos     DMSO       KO 250
#> 13 2446.167 500nM Physio Rotenone       WT 250
#> 14 3772.667 500nM Physio Rotenone       KO 250
#> 15 3505.667 500nM OxPhos Rotenone       WT 250
#> 16 2749.167 500nM OxPhos Rotenone       KO 250
df$Conc <- as.factor(df$Conc)
df$Media <- as.factor(df$Media)
df$Toxin <- as.factor(df$Toxin)
df$Genotype <- as.factor(df$Genotype)
bp <- ggplot(df, aes(x = Conc, y = Values, group = Media, color = Genotype)) +
  geom_point(aes(fill = Genotype, shape = Genotype), size = 2.5) +
  geom_errorbar(aes(ymin = Values - SD, ymax = Values + SD), width = 0.2)

bp + facet_wrap(Media~Toxin) +
  theme(strip.text.x = element_text(face = "bold"),
        axis.title.x = element_text(face = "bold"),
        axis.title.y = element_text(face = "bold")) +
  labs(x = "\nConcentration", y = "Values\n") + theme_bw()

672×480 5.76 KB

Created on 2022-05-16 by the reprex package (v2.0.1)

5

SD, I have another column with their SD, I just need the proper command to to incorporate into this graph. Each point will have its own SD. Thanks!

6

Thank you so much!!!