Updating Plots in metagenomics workflow for new iMSMS batch

[dhakim87]

After making the changes in my PR: #2 for getting linear regression working on the new batch of data, I'm running into a number of issues in fixing the heatmap and bar graph plotting code. My current issue list is:

Section 3.2.1 Nothing plots- probably dashes and dots again

Section 3.2.3 missing input file (Linear regression files were renamed but not updated everywhere):
“results/WOL_shogun/Linear_regression/disease/all/Linear_coefficient_metagenomics_species_MS_all_sex_age_bmi_fixed_house_site_random.xlsx”

(Similarly a humann2 folder that I haven’t created by this point in the file… with linear regression)

3.2.4 Probably just need to update column names to match a particular linear regression file
fix.by(by.y, y) “by” must specify a uniquely valid column.

Error on CoefHeatmap.R line 70.
Doesn’t happen with every heatmap, first heatmap in the next section works just fine.

Error on CoefHeatmap.R line 102 (condition has length > 1)

Section 3.3

treatment.seqmeta is undefined
features is undefined

Could be they’re only defined if previous parts succeed…. First reference to treatment.seqmeta is on line 993 (865 on github), so only can be defined by a load statement but I don’t see one in the crashing sections

3.3.1 humann2.path.rela is undefined. Am I missing load statements?

3.3.2 something is wrong with treatments
Possibly as simple as interferon was renamed to Interferon but I’m not convinced I’m working from similar input files to make a change here.

4 humann2.path.rela is undefined again

4.1 some null pointer

5 can’t fix the humann2 stuff because I have no treat.seqmeta

5.2 Probably need to install humann2 to run this section in bash

5.3 no such file /WOL_shogun/humann2/Akkermansia/Akkermansia_muci_genes.txt

6.1 The two loaded rda files should be included

6.1.1 No object heiseq (could be because previous sections don’t run)
6.2 Same
6.2.1 Non numeric values in data prevent log10(data) from running
6.2.2 hei2015 not found

6.3 Nothing called cofounder.anova
(next block) load("../Dietary_questionnaires_round2/rdata/dietpairsum.rda") fails (accesses outside of github)

6.4 multiple.diet not found