Suggestions

[teresho4]

Hi ImmunoMind team,

Thank you so much for such a great tool as immunarch. I tried it for my analysis and I have suggestions for possible improvements:

• Design part:

1. It would be cool if there would be several color palettes to choose from because sometimes I am not very pleased with the colors and I can't change them easily. For example, coloring for samples going from reds to blues and looks like it means something (like the colors in heatmaps or etc for continuous values), but here it is just different sample colors.
2. I think names for plots are not always consistent. For example plots with mean group values have the same names as plots with absolute values and at first, it can be confusing.

• Documentation:

1. Please add a proper description for all features, it took me a while to understand how to remove comparison from the plots because there is no .test parameter in the description for vis function.
2. In repDiversity you have a parameter normalization for Laplace correction. But it is not obvious at all why do we need it here. I was trying to find something about that, but find only cases for ML implementation and I am not very sure how to interpret it in the right way in terms of diversity calculation.

• Features:

1. Very cool feature would be to add a possibility to resample the existing samples. For example, to look at the properties in different transcriptional groups of T/B cells. In such a way, I will provide the cluster name for each cell at the repLoad function, so it can merge the samples in a different manner (patient A_cluster A, patient A_cluster B, patient B_cluster A and so on). Because now I can only make grouping for samples itself in metadata.
2. I have a question regarding your implementation of diversity indexes. Some tools use bootstrapping algorithms to subsample multiple times while calculating the diversity index. Because diversity is dependent on the sample size. As I understood, you do not have it. Do you have any type of correction on this issue or do you plan it? Rarefaction analysis has subsampling, but in immunarch it could be applied only for richness, but not other diversity measurements.
3. Very looking forward to your BCR implementation, because currently, I need to change some of the functions by my hand to make it possible to use it for BCR.

Thank you again and all the best!

[Alexander230]

Hi, Marina! :-) Thank you for your suggestions! Now I'm working on implementing BCR pipeline in Immunarch, and it's planned for the next release. I will add other suggestions as development tasks, so, if possible, we will include them in the future versions of Immunarch.

Best regards, Aleksandr

[MVolobueva]

Hi, @teresho4 ! Аs for the design part, you could easily swap color palettes using standart R tools, for example:

library(immunarch)
data("immdata")
exp_vol <- repExplore(immdata$data)
p1 <- vis(exp_vol,.by = c('Status'), .meta = immdata$meta)
p1 + scale_fill_brewer(palette = 'Dark2')

Do not hesitate to contact us with any questions further along. Good luck, Maria