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ggbarplot: Multiple groups with error bars only work with color argument #71

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j3ypi opened this issue Mar 12, 2018 · 18 comments
Closed

ggbarplot: Multiple groups with error bars only work with color argument #71

j3ypi opened this issue Mar 12, 2018 · 18 comments

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@j3ypi
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j3ypi commented Mar 12, 2018 •
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If one uses fill instead of color, one wouldn't get an error bar within the categories, but a centered error bar for each category on the x-axis. The combination of both arguments is possible though, but it's useless, since one can't see the bottom half of the error bar.

Here's a short reproducable example:

library(tidyverse)
library(ggpubr)

df <- tibble(
  iq = rnorm(100, 100, 15),
  condition = rep(c("A", "B"), each = 50),
  time = rep(c("t1", "t2", "t1", "t2"), each = 25)
)
ggbarplot(df,
      x = "condition",
      y = "iq",
      fill = "time",
      palette = "grey",
      add = "mean_se", 
      position = position_dodge(0.8))
@yfangumich
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I've had the same problem.

@j3ypi j3ypi mentioned this issue Jun 6, 2018
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@kassambara
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For customizing the error bar, you should specify the argument add.params:

ggbarplot(df,
          x = "condition",
          y = "iq",
          fill = "time",
          palette = "grey",
          add = "mean_se",  add.params = list(color = "time"),
          position = position_dodge(0.8))

@j3ypi
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j3ypi commented Jun 17, 2018

Your code doesn't work like its supposed to. It still produces error bars in the same color as the barplot, which makes it impossible to see the lower half.

What I want is this:

df %>% 
  group_by(condition, time) %>% 
  summarise(IQ = mean(iq),
            se = sd(iq) / sqrt(n())) %>% 
  ggplot(aes(x = condition, y = IQ, fill = time)) +
  geom_bar(width = 0.85, position = position_dodge(width = 0.9), stat = "identity") +
  geom_errorbar(aes(ymin = IQ - se, ymax = IQ + se),
                width = .2,                   
                position = position_dodge(0.9)) + 
  scale_fill_grey() +
  theme_pubr()

The problem wouldn't exist, if the color argument would work intuitivly like fill.

@kassambara kassambara reopened this Jun 17, 2018
@cnnmat
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cnnmat commented Aug 2, 2018

Same problem here.

@kassambara
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With the latest developmental version of ggpubr, you can do this:

# Required packages and demo data
library(tidyverse)
library(ggpubr)
df <- tibble(
  iq = rnorm(100, 100, 15),
  condition = rep(c("A", "B"), each = 50),
  time = rep(c("t1", "t2", "t1", "t2"), each = 25)
)


# Visualization
ggbarplot(df, x = "condition", y = "iq", 
          fill = "time", palette = "grey",
          add = "mean_se",  add.params = list(group = "time"),
          position = position_dodge(0.8))

rplot45

@j3ypi
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j3ypi commented Aug 12, 2018

Works like a charm - thanks!

@kassambara
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so we can close the issue

@sophiahng
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It does not work for me.
It produces error codes
Error in (function (p, add = NULL, color = "black", fill = "white", width = 1, :
unused argument (group = "time")
What is the problem?

@j3ypi
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j3ypi commented Aug 21, 2018

You have to install the current development version via

devtools::install_github("kassambara/ggpubr")

@sophiahng
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Problem solved. Thanks!

@cnnmat
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cnnmat commented Aug 24, 2018

Merci beaucoup !

@dkagro1991
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Yielddata.xlsx
i want to create a barplot on data yld and yld2 (sheet2) in r studio after importing my excel sheet into r studio. I am foloowing the step provided by you but not able to creat one. plz help me with the steps and codes. Thankyou

@kassambara
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grps column should be organized as highlighted in red.

groups

@elenichri
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Hello,
I have a similar issue but with adding points after doing the barplot: The points are added in the middle of the group. I want however to add them at each bar of the group. So the x for the points should be different from the x for the x for the barplot. How can I do that? Here is my code:

ggbarplot(melted_fig4a.dmso, x = 'drug', y = 'value', width=0.8, add = c("mean_sd"), add.params = list(color='black', group='compound_concentration'), font.xtickslab = 20, font.x=22, font.ytickslab = 20, font.y=22, ylim=c(0,15), color='compound_concentration', #no, group by concentration fill='compound_concentration', position=position_dodge(0.8), palette='grey', x.text.angle=90) + geom_point(size=2, data= melted_fig4a.dmso, aes(x=treatment, y=value))

This adds the points in different columns AFTER the bars of each group

Here are the top 15 lines of the melted_fig4a.dmso
treatment compound_concentration replicate value drug
None 1 rep1 0.33 None
Dima 1 1 rep1 0.73 Dima
Dima 10 2 rep1 1.03 Dima
Dima 100 3 rep1 2.49 Dima
Quin 1 1 rep1 0.74 Quin
Quin 10 2 rep1 0.46 Quin
Quin 100 3 rep1 0.53 Quin
Colc 0.0025 1 rep1 1.35 Colc
Colc 0.005 2 rep1 2.41 Colc
Colc 0.01 3 rep1 1.53 Colc
Meb 0.05 1 rep1 0.38 Meb
Meb 0.1 2 rep1 1.11 Meb
Podo 0.005 1 rep1 0.68 Podo
Podo 0.01 2 rep1 1.02 Podo
Dino 1 1 rep1 0.74 Dino

I would very much appreciate your help

Eleni

@dkagro1991
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dkagro1991 commented May 24, 2023 via email

@marinaaa118
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marinaaa118 commented May 25, 2023 via email

@dkagro1991
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dkagro1991 commented May 26, 2023 via email

@marinaaa118
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marinaaa118 commented May 26, 2023 via email

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8 participants
@yfangumich @kassambara @elenichri @sophiahng @j3ypi @cnnmat @dkagro1991 @marinaaa118