I hope all are fine, 1 : I have this taxonomy bar plot (attached ) set on level 7 which is supposed to show species , for instance in the first line of legend there is Staphylococcaceae ( family : level 6 ) Staphlylocococcus (genus: level 7 ) ,It is not really up to species level …
level 7 is the last level. As in the Moving pictures tutorial, level 2 has been introduced as phylum ,
If level 2 is phylum level 7 should be species so it should show the species of Staphlylocococcus like S.
aureus or other species , you know why it is not like this?
Why there are too many similar colors in legends when you scroll down with different category and relative frequency? and why some columns doesn’t have any taxonomic rank like this one in the legend 'k_Bacteria; ; ;_ and some are not fully covered the taxonomic rank from phylum to genus ?
2: How I can use this taxonomy bar plot in the publication because there is no option to download all the legends which is a lot and the plot together but there are some option like SVG ,SVGlegend and CSV (still I do not know the use of them) sounds like all are associated with internet browser when they are downloaded and not an image or something which can be used in publication,
3: What other things I can do with the result of QIIME2 after this step and getting the taxa bar plot. I just follow the Moving picture tutorial and tried to do relatively same steps on my samples. Now I want to do more visualization if possible, also I do not have too many information in my metadata file just sample id and disease category (attached) , what do you suggest ?
This plot is showing level 7 (i.e., species level) — just not all are assigned to species, and some are assigned to species that have no species-level annotation in the reference database. See this post and search elsewhere on this forum for more details.
With such a large number of species, there is no way to design a color scale that can accommodate all of them. Even if you did, e.g., use a color gradient, human eye cannot easily distinguish so many colors. You can choose different color palettes (with up to 20-some colors), which have been designed (by others not ) for color-blind accommodation and general readability. These are the color palettes available in the plotting packages that uses to generate these plots.
SVG is not browser-specific. You can open and edit SVGs with all sorts of image editing software — try Adobe Illustrator or Inkscape, maybe gimp would work too.
Given your concerns about the colors, though, I recommend that you download the data as CSV, filter out very low abundance taxa and others that you don't want to plot, and then plot either using R or even in excel so that you can customize each individual color. (of course you can also do the filtering in , then use image editing software to manually recolor bars).
Check out the other tutorials — moving pictures is just a taste of some basic analyses. Check out the overview tutorial, which gives a good beginner-level overview of many different other methods and tutorials.
Or see here for a list of all available plugins and plugin actions.
Thank you VERY MUCH for your reply ,
I have downloaded SVG (bars), SVG (legends) and CSV, u recommended to filter out the low abundance taxa and then plotting using excel or R with the rest taxa. I opened the csv file in excel, too many zero (attached) it means no taxa has been assigned for , Should I filter all the zeros, I tried but it is not practical if I want to do plotting in excel ? how I can make sure particular taxa has been low and then filter it?
Do you have same posts using image editing software on SVGs and how to do it as I couldn’t find any .
filter using QIIME 2 with qiime feature-table filter-features, and then generate a barplot and export the data if needed.
SVG can be opened in adobe illustrator and inkscape — beyond that you can search around on this forum for related posts. Other image editing software might not accept this format. Inkscape is free as far as I know if you don’t have an adobe license.