Thank you for the video , it was really informative and simple to execute 😇😇
@thepandemics56143 жыл бұрын
I used to visualise clustering using cytoscape......just try this.....
@Guruprasad_A3 жыл бұрын
Ok
@SonuLangaya2 жыл бұрын
Hi, Is there any introductory tutorial on the same. Like how it is done in Cytoscape.
@thepandemics56142 жыл бұрын
@@SonuLangaya well just installs Cytoscape and transforms the matrix according to individual interaction. directly fetch the file and you will find the tocher graph according to inter and intra values
@PlantBreeding_is_my_passion3 жыл бұрын
very good hard work and wonderful video thanks bro
@minhalsheikh6335Ай бұрын
Sir how to create the cluster distances in cluster diagram
@Guruprasad_AАй бұрын
For Mahalanobis D square stats we won't get clusters diagram.
@jaybabariya1413 жыл бұрын
Thank you for this amazing video. I have one doubt that how to find cluster mean table using R ?
@Guruprasad_A3 жыл бұрын
If the output was in list. we can use the aggregate function (refer last part of my cluster analysis video), unfortunately it's not in list. so it's difficult to use aggregate function because we need to create list manually and it takes more time, so add an extra columns before genotypes and fill it with cluster membership (1,2,3. .......) Whatsoever for you and sort them based on cluster membership Column and calculate mean by adding a extra row at the end of each cluster.
@asingh93173 ай бұрын
Kindly suggest when no. Of genotypes are less than no. Of traits, these codes are not giving results. It gave best results when genotypes were either more in number or equal to no. of observations.
@Guruprasad_A3 ай бұрын
Not soo, i think.
@asingh93173 ай бұрын
@@Guruprasad_A can we work for less no of genotypes and more observed traits?? If so then I have to check my data
@Guruprasad_A3 ай бұрын
@@asingh9317 Sure, but inorder to study we need more genotypes.
@asingh93173 ай бұрын
@@Guruprasad_A got it...thanks alot🍁🍁
@prawalpsverma49038 ай бұрын
Where is as.factor function ?
@Guruprasad_A7 ай бұрын
It's built in base r package.
@snehasivasubramani53452 ай бұрын
I have an doubt. In manova I cannot get the results. It shows there are more variables ie..26
@Guruprasad_AАй бұрын
Check the name of replicates in genotypes or confirm in the code whether you the selected genotypes variable correctly.
@s.husain6125 Жыл бұрын
Hello sir code workig till covar calculation but when i run imp
@Guruprasad_A Жыл бұрын
It means there is a lot of correlation in the variables of your dataset. Please check the correlation among the variables and try to remove those variables.. For example you find correlation in days to first flower and days to fifty percent flowering etc...
@shivangitare7102 Жыл бұрын
sir, what is the script for find out the cluster mean value from tocher method
@Guruprasad_A3 жыл бұрын
Hi, everyone don't hesitate to ask your doubts here...... I will try to answer them.
@prawalpsverma49038 ай бұрын
Sir Please tell me how to make image of inter cluster and intra cluster
@amitrana7342 жыл бұрын
Sir can you suggest how i can make cluster diagram using any other software if not possible in R. Please also tell how i can make tocher based dendrogram in R
@Guruprasad_A2 жыл бұрын
You can use window stat software if you have it
@vikramana77964 ай бұрын
Sir can you explain elaborately, how to do cluster means
@Guruprasad_A4 ай бұрын
Group them individually / seperate the groups in different Excel sheet then take average.
@Guruprasad_A2 жыл бұрын
Use “~” tilde not the “-” after dv~
@sukumartaria35822 жыл бұрын
Can we get p- value of each cluster based on mahalanobis distance or can we get p-value of each cluster in LDA analysis?? If yes put the code
@Guruprasad_A2 жыл бұрын
No
@dibsohbordoloi79523 жыл бұрын
Sir I have found error in code manova calculating part, the r studio showed error in is.factor(x) 'Genotype' not found
@Guruprasad_A3 жыл бұрын
Is there any missing genotypes ? Please do check the name of genotype column in your dataset ?
@aswathiap55922 жыл бұрын
Just a doubt..Can we do univariate analysis for clustering when we have n number of genotypes studied for say m number of traits?
@Guruprasad_A2 жыл бұрын
Univariate = one variable, Multivariate = Multiple or more than one variable, In our context, Variable = Trait.
@rakeshgowda79822 жыл бұрын
The video was very clear. I have one error while executing the code summary(mod), and it was "Error in summary.manova(mod) : residuals have rank 3 < 8", can you please help me in rectifying this error.
Bro how to plot the dendrogram we are getting the clusters na how to plot them can we get that process
@Guruprasad_A Жыл бұрын
Dendrogam is not possible with tocher method.
@thomasmuse583 Жыл бұрын
is it possible to analyze over location lattice design experiment using the explained script?
@Guruprasad_A Жыл бұрын
If you have replication yes
@nehabelsariya5898 Жыл бұрын
Thank you so much sir for this video. I would like to ask you about the diagram of tocher method?? How can we make that?
@Guruprasad_A Жыл бұрын
We can't make it, it won't be that much appropriate because it's not a hierarchical method of clustering
@nehabelsariya5898 Жыл бұрын
@@Guruprasad_A how you make last in video. diagram of 169 genotype by tocher method
@rounakkumar6259 Жыл бұрын
How to draw dendogram after modified tocher method ..plse help
@Guruprasad_A Жыл бұрын
Not possible in this package.
@aswathiap55922 жыл бұрын
Sir, I'm getting error in D2.dist step. I did as said in video but I'm getting error saying dimension is incompatible, I have 12 characters and 18 genotypes, please help...
@Guruprasad_A2 жыл бұрын
I think there is a problem with number of variables, which you have considered for calculating variance and covariance matrix and the number of variables in average data.
@aswathiap55922 жыл бұрын
Thank you
@deepikachandrasekaran355411 ай бұрын
Sir, in the R software while doing linear discriminant analysis, it is showing that figure margin is too large. Is there any solution?
@Guruprasad_A11 ай бұрын
Try taking out one variable at a time and re do analysis until u find out the variable which might be that error…
@deepikachandrasekaran355411 ай бұрын
@@Guruprasad_A Thank you sir, will try and let u know....
@deepikachandrasekaran355411 ай бұрын
@@Guruprasad_A Sir I tried the method u said, but the same error is happening, it is showing plot.new (): figure margins too large
@yellankinaveen24962 жыл бұрын
Error in model.frame.default(formula = dv ~ as.factor(genotype) + as.factor(Repl), : variable lengths differ (found for 'as.factor(genotype)') In addition: Warning message: In xtfrm.data.frame(x) : cannot xtfrm data frames > i am facing this error place help to solve this problem
@Guruprasad_A2 жыл бұрын
That error is because, the number of genotypes and replications are not same. Check some of them might be missing
@yellankinaveen24962 жыл бұрын
@@Guruprasad_A sir i am beginner in the Programming can you tell me how to read the error
@Guruprasad_A2 жыл бұрын
@@yellankinaveen2496 check if all the genotypes and replications are present are not
@khushwantb.choudhary81572 жыл бұрын
how can we do D2 of two environment data (as pooled)/ for example control and drought environment, i want to calculate d2 clustering for pooled data involving both the envs. Kindly tell me.
@Guruprasad_A2 жыл бұрын
Check this out once in STAR, PB tools. There we may get an option.
@Guruprasad_A2 жыл бұрын
It's better to do it separately for both environment.
@jaybabariya1413 жыл бұрын
Hello sir, I found error in summary.manova(mod) : residuals have rank 17 < 18 I have 18 characters. Please suggest what does that mean? And what I have to do ?
How to generate dendrogram using tochers method in r studio sir
@Guruprasad_A2 жыл бұрын
Cluster diagram is not possible in this package
@s.husain61252 жыл бұрын
How to analyse D square with 2 year of data of fied trail sir
@Guruprasad_A2 жыл бұрын
Take multiple year data as replication.
@sasipriyas30122 жыл бұрын
sir, can you make a video on metroglyph analysis
@Guruprasad_A2 жыл бұрын
As of now I am busy with my course work, I look into it later.
@saujanbashyal12472 жыл бұрын
Can we define the number of clusters in tocher's method? I am getting 3 clusters but if i want 4 clusters, how would i do that?
@Guruprasad_A2 жыл бұрын
You can opt for k means cluster
@Guruprasad_A2 жыл бұрын
Or try alternative tocher method
@akshatahattiholi8016 Жыл бұрын
Hello sir... Sir i didnt get how to find cluster means...can u explain me sir??
@Guruprasad_A Жыл бұрын
Need to calculate manually, by seperating clusters in an Excel sheet.
@akshatahattiholi8016 Жыл бұрын
Sir, Separating clusters means: of single trait the genotypes present in the one cluster have to take the average ???
@Guruprasad_A Жыл бұрын
Add one more column to data mention the cluster number, then sort according to cluster number and take average.
@akshatahattiholi8016 Жыл бұрын
Ok sir...got it...Thank you sir...
@bhumikasinghlodhi6632 Жыл бұрын
thanks for the video. I am getting error after executing manova command, Error in `[[
@Guruprasad_A Жыл бұрын
I think it's a problem with your dataset or you might have mis selected the variables.
@bhumikasinghlodhi6632 Жыл бұрын
@@Guruprasad_A I have check the data many times but couldn't get the mistake. can you help me in finding the mistake
@Guruprasad_A Жыл бұрын
@@bhumikasinghlodhi6632Send the dataset, I am quite busy as of now, but I will try to clarify it by next Wednesday.
@bhumikasinghlodhi6632 Жыл бұрын
Please provide me your email
@Guruprasad_A Жыл бұрын
gthings1597@gmail.com
@vijaydunna8088 Жыл бұрын
Dear The Outlier, Thank you for the very good video. I am facing a problem. The total number of clusters formed using this code is only 2. While the same data was analysed using windowstat the number of clusters are 25. why this difference?
@Guruprasad_A Жыл бұрын
In both the methods also you are getting 2 clusters.
@vijaydunna8088 Жыл бұрын
@@Guruprasad_A yes both tocher and modified tocher
@Guruprasad_A Жыл бұрын
Can you able to check distance matrix sir, whether both are some or not.
@niharikadhuliya6219 Жыл бұрын
@@Guruprasad_A hii
@sathyarajdurai394 Жыл бұрын
Cluster mean is where? Bro
@Guruprasad_A Жыл бұрын
You have to calculate manually by grouping the varieties or treatments separately based on their clusters identity in an excel sheet.
@gayatrikumawat67032 жыл бұрын
please mention code for last cluster diagram
@Guruprasad_A2 жыл бұрын
We can't get a cluster diagram in this package. But for the last diagram which depicts inter and intra cluster distance we need to create manually in Microsoft power point.
@sukumartaria35822 жыл бұрын
Any R code for plotting cluster diagrams with the Tocher method?
@Guruprasad_A2 жыл бұрын
No, sorry
@sukumartaria35822 жыл бұрын
If any reference code is there for the same...plz update here
@Guruprasad_A2 жыл бұрын
@@sukumartaria3582 ok
@dibsohbordoloi79522 жыл бұрын
Sir how we draw the diagram of tochers clustering diagram please help me
@Guruprasad_A2 жыл бұрын
In this package we can't generate a cluster diagram.
@dibsohbordoloi79522 жыл бұрын
@@Guruprasad_A is there any package sir
@Guruprasad_A2 жыл бұрын
@@dibsohbordoloi7952 Nope, as per my knowledge
@truongphu74073 жыл бұрын
Thanks author to deliver a valuable video, could you tell me how to create Fig.3 (Inter cluster and intra cluster distance...) in the end of the clip? Thanks again
@Guruprasad_A3 жыл бұрын
Imagine you have got 5 no of clusters then draw Pentagon which will be having 5 sides at intersection you have to draw a circle so totally 5 circles, later label the 5 circles serially within them mention the intra cluster distance. Later connect all the circles then for example on the line which connects the 5th and 3rd circle (which represents inter cluster distance between 3rd and 5th cluster) mention inter cluster distance between 3rd and 5 th cluster in the same way do this inbetween other circles.
@truongphu74073 жыл бұрын
@@Guruprasad_A Thanks for your prompt reply. Did you mean we need to create manually?
@Guruprasad_A3 жыл бұрын
Yup
@sourabhkumar12852 жыл бұрын
@@truongphu7407 How to create manually?
@maramakashreddy68192 жыл бұрын
Sir, help me to solve this error Error in is.factor(x) : object 'Genotypes' not found
@Guruprasad_A2 жыл бұрын
Check the name of genotypes column in Excel sheet and confirm that same as mentioned in R studio also. Remember R is case sensitive
@maramakashreddy68192 жыл бұрын
Both are same sir even though it is showing the same error
@senaitlegesse17092 жыл бұрын
how to f ix this problem please i got same probllem
@Guruprasad_A2 жыл бұрын
Check the name of the genotypes column what is there in Excel and in our video they have to be same.
@mysterious97182 жыл бұрын
How did you solve that sir.. Even I have the same error though everything is perfect...
@saujanbashyal12473 жыл бұрын
Isn't it necessary to scale the data? I think we should scale both dv matrix and averaged data frame
@Guruprasad_A2 жыл бұрын
Calculating paired Mahalonobis distance is kind of scaling only.
@saujanbashyal12472 жыл бұрын
@@Guruprasad_A Will it be valid if i use: mod
@Guruprasad_A2 жыл бұрын
As per the information what I got from the original author, I did made this video. I hope you follow what I have shown in video
@Guruprasad_A2 жыл бұрын
I hope this helps you to understand scanning is as good as calculating Mahalonobis distance stats.stackexchange.com/questions/210155/mahalanobis-distance-and-feature-scaling towardsdatascience.com/mahalonobis-distance-and-outlier-detection-in-r-cb9c37576d7d
@dgeethanjali71772 жыл бұрын
Please can you send codes
@Guruprasad_A2 жыл бұрын
Check the description
@sasipriyas30123 жыл бұрын
Sir, can you please share how to do the analysis without replicated data ( augmented design)
@Guruprasad_A3 жыл бұрын
We can't do tocher method of clustering for non replicated data.
@Guruprasad_A3 жыл бұрын
Try Ward min variance method insted, as shown in my cluster analysis video
@sasipriyas30123 жыл бұрын
Thank you sir 👍
@RamendraSarma2 жыл бұрын
@@Guruprasad_A why Ward minimum variance method
@Guruprasad_A2 жыл бұрын
@@RamendraSarma It's subjective you can use any other methods such as average, complete etc... But most often used method is ward minimum variance method when it comes to hierarchical clustering in genetic diversity studies using morphological data.
@rnsarma88762 жыл бұрын
can you share the codes?
@Guruprasad_A2 жыл бұрын
Sure give me your email I D
@Guruprasad_A2 жыл бұрын
or Just send me a message to gthings1597@gmail.com
@basazinewdegu41812 жыл бұрын
Thank you Sir for this very important video. I have got a problem while I was doing my data on percentage contribution. The error said: Error in solve.default(cov) : system is computationally singular: reciprocal condition number = 1.54415e-19 How can I amend/correct it? Please, give me your valuable comment.
@Guruprasad_A2 жыл бұрын
It's seems your data is having too much correlation between the variables, please reduce it and see.