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cropped and incomplete "genus" stacked barplot generated with R

Hi friends, I am using R phyloseq software package for visualisation of data. I don't know why am I getting an incomplete stacked barplot at "genus" level like this (attachment) . I am getting a complete and a nice barplot at the class and Phylum level though. I am using the following code:

# setting the seed to one value in order to created reproducible results

set.seed(1)  

# scaling the human data to the smallest samples. Note: rngseed is similar to set.seed

human_scaled <- rarefy_even_depth(human_data, sample.size=52975, replace=FALSE, rngseed = 1) 

# Make a data frame with a column for the read counts of each sample

plot_bar(human_scaled, fill="Genus")

I am new in R and metagenomic data analysis. And, don't know how can I get the full "genus" level barplot. Can anyone please help me out?

Thanks and Regards, DC7

mothur 16s r software error phyloseq
• 1,948 views • link
written by dpc dpc

Please host the image on public server. Current location asks for user's google credentials. plot_bar(myData, fill="Genus") is supposed to give you Genus level distribution (color the relative abundance at Genus level). Could you explain what you are looking for with an example?

• 0 views • link
written by cpad0112 cpad0112

Sir/Madam, Can you please check this link?

Actually, I want to see the relative abundance of the genus for each sample through a stacked barplot.

• 0 views • link
written by dpc dpc

I think legend squished the plot. Turn off legend and check if you can see the stacked the bar plot. What you are seeing is the legend of the plot (as I understand from the image, posted). Try some thing like this:

plot_bar(human_scaled, fill="Genus")+
theme(legend.position = "none")
• 0 views • link
written by cpad0112 cpad0112

Many many thanks cpad0112. I am getting a complete image now like this. Great relief!!! Can you please tell me why I am seeing that black bands in the image. i mean between two genus some bands are thin and some are considerably very thick.

Thanks DC7

• 0 views • link
written by dpc dpc

that is border around each genus. If you look at the legend, you would see that each block (genus) is surrounded by black border. see adding +geom_bar(stat="identity") works. But this is not correct. There is a better and correct way to do that. Please look at the package manual.

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written by cpad0112 cpad0112

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