cropped and incomplete "genus" stacked barplot generated with R

Question

[dpc]

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

[cpad0112]

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?

[dpc]

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.

[cpad0112]

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")

[dpc]

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

[cpad0112]

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.