Plotting bargraph with SE and alphabets in R | LSD test
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- Опубликовано: 12 июл 2024
- You can learn how to map a bar graph with main and interaction effects in this video. The following subjects will be included in the video tutorial:
1:10 Importing data and formatting variables
1:55 Analysis of variance model
2:42 LSD mean comparison test
4:29 Arranging treatment groups from LSD test
5:28 Computing mean and standard error
6:28 Visualizing bar plots
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Download Links
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Download R-script & data file - visit this blog:
agroninfotech.blogspot.com/20...
Updated blog post link:
www.agroninfo.com/bar-plot-se...
R is free software and you can download it from the link given below
www.r-project.org/
Download link for R studio
www.rstudio.com/products/rstu...
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If you have any question please comment below.
Thanks for watching this video.
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Man you saved me!! I love your videos and your channel is full of useful content for a newbie in R like me. Keep it going,
Best regards from Colombia,
Rafael
Thank you dear
Thank you. I browse your blog and find this video. Now I have understood these R codes, and I am able to visualise the results of two-way ANNOVA analysis.
You are most welcome
Excelente video, espero que hayan mucha mas en el futuro, muchas gracias.
Thanks
Thank you so much for this video! I have been having issues with attaching letters above error bars to represent the statistical significance and this video helped me so much!!!
You are most welcome. Thank you for appreciation.
Very interesting. Thanks so much
You are welcome
Very helpful, thanks
You are most welcome
great video thanks
Thank you
Thanks AGRON
Thanks for your support 👍
Excellent video. Could you inform me about the script for calculations for lsd value instead of groups? Thanks in advance
Thank you! I have a problem in the interaction term at 4:10 when trying to use my code: "Error in soil:ion : Argument NA/NaN"" -> I had to build a new variable which considers both parameters (is this correct)
Mask the components data object before ANOVA using below command and then it will work.
data$soil = as.factor(data$soil)
data$ion = as.factor(data$ion)
attach(data)
Then proceed with ANOVA and mean separation test
thank you, sir. Do you help me with the same issue with boxplot instead of bargraph ? Thank you so much.
Okay just share your Rscript code and data at agroninfotech@gmail.com
Very interesting lectures. Thank you in advance! Using this video, I was tried my data to do the LSD but during the interaction effect (i.e. LSD_AB; it shows an error-Genotypes: TRT: NA/NaN argument). Can you please help me ?
Can you please send me str(data) result at agron.infotech@gmail.com
R is case sensitive and make sure while using the interaction term in trt argument (trt = factorA : factorB,) you entered the variable names correctly.
For more details also visit this blog post: agroninfotech.blogspot.com/2020/08/barplot-for-main-and-interaction.html
I sent it to your email. kindly please check it!
See inbox please
@@AGRONInfoTech I have the same error please help me. I'm worried. I will wait for your answer.
this is exactly what i was looking for...but im having trouble at the geom_errobar(aes .. can you please give a link the example you excecuted in r? please
You can download R script and example data set from the link provided in description. When you will open this link a blog post will appear and at the end of this post you will get the download links.
@@AGRONInfoTech ooh thanks a lot..it worked!
You are most welcome
I have a problem in the interaction term at 4:10 when trying to use my code: "Error in soil:ion : Argument NA/NaN"" .....what i have to do?
Before ANOVA please run following commands:
data$soil = as.factor(data$soil)
data$ion = as.factor(data$ion)
attach(data)
Where data specify object containing data set which was imported from excel sheet.
If still have issues please let me know
Hi
Thanks for your efforts. It is very helpful and easy to follow. Could you please give me the code on how can I give LSD Bar (Interaction LSD Value) at the top of the graph?
ruclips.net/video/s8MJdOTnrCA/видео.html you can see an example in this vedio
Please click the link given in description of this video. It's a blog post link where you will get all details and download links for R script and data file is given at the end of each the post.
Would it work as well with kruskal-wallis or wilcoxon when normality is not achieved?
You may try it please
Thank you very much for the helpful instruction. It is very helpful! I am trying to run the code, however, I do see the same error as others saw before: Although I put the comment before I run the Anova as:
(data$genotype=as.factor(data$genotype)
(data$gender=as.factor(data$gender)
attach(data)
I receive the error that said " the following objects are masked from data: activity,gender,genotype?
I need help figuring out where I am wrong. Please help me to fix it.
This is not an error. It's just a message when you use the attach() function. If you are still not clear then share with me the script and data at agroninfotech@gmail.com and I shall send you the required output
I have tried to use the same method for RBD anova followed by LSD post hoc and lastly bargraph with errorbar and SE. I have 18 treatments. However after plotting the treatment order was not same as input order. how to rearrange it?
I have received your email and shall work on the files you have provided. I shall return the files with corrected codes on Sunday.
@@AGRONInfoTech many many thanks
Sir, Can you share the video for error bars and significant letters for strip plot design.
I just went through your email. I think there is some issue with the codes that you have used to create this barplot. I can better correct the codes if you can share the data file and script you have used to create this plot.
dear professor can you use the methode for split plot for putting the letter a, b, c
Sure I shall add a video later. However if you need it urgently you can share your dataset and details at below email and I shall send you script with analysis and visualizing variables with error and letters on each bar using ggplot2 package.
agron.infotech@gmail.com
Give me your email adress i will share to you the data excel and CV
Thank you so much for this video however an Error occurred when the LSD_AB line run: "Error in genotype:gender : NA/NaN argument
In addition: Warning messages:
1: In genotype:gender :
numerical expression has 18 elements: only the first used
2: In genotype:gender :
numerical expression has 18 elements: only the first used
3: In data.frame(y, trt) : NAs introduced by coercion
4: In data.frame(y, trt) : NAs introduced by coercion" could you help me to understand it?
Before ANOVA please run following commands:
data$genotype = as.factor(data$genotype)
data$gender = as.factor(data$gender)
attach(data)
Where data specify object containing data set which was imported from excel sheet.
If still have issues please let me know
thank you instructor, my analysis shows " object plot A not found" don't show plot or bargraph after " print(p1) run
Sorry for the delay in response. You can share your script at agron.infotech@gmail.com
MeanSE_A = data %>%
+ group_by(pho) %>%
+ summarise(avg_A = mean(val),
+ se = sd(val)/sqrt(length(val)))
Error in UseMethod("group_by") :
no applicable method for 'group_by' applied to an object of class "function"
PLEASE RESOLVE
I couldn't access R script and example data from the links you provided. Please let me know how to get it. Thanks.
Share your email address and i shall send you through email
@@AGRONInfoTech k.mintun08@gmail.com
See your inbox please
@@AGRONInfoTech i.balume@gmail.com , please sent to me too this is very important
@@isaacbalume8771
Error came out after running:
LSD_AB = LSD.test(y = activity,
trt = genotype:gender,
DFerror = aov.res$df.residual,
MSerror = deviance(aov.res)/aov.res$df.residual,
alpha = 0.05,
p.adj = "bonferroni",
group = TRUE,
console = TRUE)
The problem is:
Error in genotype:gender : NA/NaN argument
In addition: Warning messages:
1: In genotype:gender :
numerical expression has 18 elements: only the first used
2: In genotype:gender :
numerical expression has 18 elements: only the first used
3: In data.frame(y, trt) : NAs introduced by coercion
4: In data.frame(y, trt) : NAs introduced by coercion
How can I do two dependent variables within one bar chart
I shall create a separate video on this soon
@@AGRONInfoTech Ok I wait for that
How can I do this with just 1 group? just with "Female" for example.
You can filter data before proceeding for analysis. Use below command:
library(tidyr)
data2 = filter(data, gender == "Female")
Then work on data2 to plot a graph
I don't know where I did wrong." colon.pc" data type is numeric
> comp1 = LSD.test(y=colon.pc,
+ trt = Substrate,
+ DFerror = m1$df.residual,
+ MSerror = deviance(m1)/m1$df.residual,
+ alpha = 0.05,
+ p.adj = "bonferroni",
+ group = TRUE,
+ console = TRUE)
Error in "aov" %in% class(y) : object 'colon.pc' not found
The error indicates you have not attached the components of data file using attach() function. If you are using y argument (y = colon.pc) where colon.pc is response variable name then you need to do either of the following:
Use attach(data) to attach the colon.pc component of the data file if you are just trying to simply use the name of the variable
Use y = data$colon.pc if you are not using attach function.
Hope this will fix the error. If you still have the error please let me know.
@@AGRONInfoTech It works !!! Thanks heaps
You are welcome
Can you help me with my data in split split plot
Why not. Just let me know what issue you are facing in this analysis
Thank you for your teaching. I wanted to download the data file, but it was not possible. So, I made a data frame that is the same as your data. I hope it is also helpful to others. If you feel uncomfortable, I will delete this comment
data
Thank you. I shall try to embed data set and Rscript so that login may not be required to download these files.
Hi, Kindly assist. I've been analyzing the data using your guidance but i'm getting "NA/NaN argument" at the point of analysing the interactions. Below is the command for interaction between clone and season and i'm getting the error message so i can't proceed with analysis. LSD_AB=LSD.test(y=rootweight,trt=clone:season,DFerror=aov.res$df.residual,MSerror=deviance(aov.res)/aov.res$df.residual,alpha=0.05, p.adj="bonferroni",group=TRUE,console=TRUE)
Send me data and code you have used at agroninfotech@gmail.com