Last updated: 2021-06-18

Checks: 4 3

Knit directory: MS_lesions/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: uncommitted changes

The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Environment: objects present

The global environment had objects present when the code in the R Markdown file was run. These objects can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment. Use wflow_publish or wflow_build to ensure that the code is always run in an empty environment.

The following objects were defined in the global environment when these results were created:

Name	Class	Size
broad_cols	character	1.7 Kb
broad_ord	character	808 bytes
broad_short	list	2.1 Kb
coef_regex	character	136 bytes
coloc_f	character	168 bytes
cols_fn	function	402 Kb
confounders	character	328 bytes
disease_cols	character	864 bytes
disease_ord	character	376 bytes
do_muscat_run	function	6.7 Kb
gsea_regex	character	168 bytes
gtf_f	character	168 bytes
labels_f	character	168 bytes
lesion_cols	character	1.4 Kb
lesion_ord	character	680 bytes
load_labelled_dt	function	10.7 Kb
load_meta_dt	function	25.8 Kb
load_names_dt	function	101.2 Kb
lof_f	character	232 bytes
magma_f	character	136 bytes
matter_cols	character	464 bytes
matter_ord	character	176 bytes
nice_cols	character	1.9 Kb
outlier_cols	character	464 bytes
outlier_ord	character	176 bytes
path_dir	character	136 bytes
path_names	character	1.5 Kb
paths_list	list	2.3 Kb
plot_coefficients_scatter	function	247 Kb
plot_design_pca	function	229 Kb
plot_gsea_dotplot	function	432.7 Kb
plot_gsea_results_inter	function	52 Kb
plot_gsea_results_intra	function	61.1 Kb
plot_logfc_distns	function	133.1 Kb
plot_mds	function	643.9 Kb
plot_mds_heatmap	function	265.6 Kb
plot_n_signif_barplot	function	247.3 Kb
plot_n_signif_heatmap	function	161.9 Kb
plot_random_effect_pca	function	811.8 Kb
plot_top_genes_heatmap_fn	function	532.6 Kb
plot_upset	function	222 Kb
q	function	1008 bytes
render_muscat_results	function	72.1 Kb
run_descs	list	3.6 Kb
run_muscat_and_gsea	function	95.9 Kb
save_dir	character	136 bytes
sex_cols	character	608 bytes
sex_ord	character	248 bytes
soup_dir	character	136 bytes
source_cols	character	896 bytes
source_ord	character	408 bytes
test_ord	character	1 Kb
tfs_f	character	168 bytes
unique_labs	character	720 bytes
unique_ls	list	712 bytes
var_cols	character	2.5 Kb
var_types	character	184 bytes

Seed: set.seed(20210118)

The command set.seed(20210118) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: detected

The following chunks had caches available:

plot_coefficients_scatter
plot_de_barplot
plot_design_pca
plot_gsea_results_confounders
plot_gsea_results_inter_confounders
plot_gsea_results_inter_test
plot_gsea_results_intra_confounders
plot_gsea_results_intra_test
plot_gsea_results_test
plot_heatmap_sep
plot_logfc_distns
plot_magma_genes
plot_mds_all
plot_mds_sep
plot_no_signif_by_contrast
plot_random_effects
plot_top_genes_confounders
plot_top_genes_test
plot_upsets_by_cluster
plot_upsets_by_coef
print_desc
print_run
session_info
session-info-chunk-inserted-by-workflowr

To ensure reproducibility of the results, delete the cache directory ms10_muscat_template_broad_cache and re-run the analysis. To have workflowr automatically delete the cache directory prior to building the file, set delete_cache = TRUE when running wflow_build() or wflow_publish().

File paths: relative

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Repository version: 856df8d

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 856df8d. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rprofile
    Ignored:    .Rproj.user/
    Ignored:    ._.DS_Store
    Ignored:    ._MS_lesions.sublime-project
    Ignored:    .log/
    Ignored:    MS_lesions.sublime-project
    Ignored:    MS_lesions.sublime-workspace
    Ignored:    analysis/.__site.yml
    Ignored:    analysis/figure/
    Ignored:    analysis/ms02_doublet_id_cache/
    Ignored:    analysis/ms03_SampleQC_cache/
    Ignored:    analysis/ms04_conos_cache/
    Ignored:    analysis/ms05_splitting_cache/
    Ignored:    analysis/ms06_sccaf_cache/
    Ignored:    analysis/ms07_soup_cache/
    Ignored:    analysis/ms08_modules_cache/
    Ignored:    analysis/ms09_ancombc_cache/
    Ignored:    analysis/ms09_ancombc_clean_1e3_cache/
    Ignored:    analysis/ms09_ancombc_clean_2e3_cache/
    Ignored:    analysis/ms10_muscat_run01_cache/
    Ignored:    analysis/ms10_muscat_run02_cache/
    Ignored:    analysis/ms10_muscat_template_broad_cache/
    Ignored:    analysis/ms10_muscat_template_fine_cache/
    Ignored:    analysis/ms11_paga_cache/
    Ignored:    analysis/ms12_markers_cache/
    Ignored:    analysis/ms13_labelling_cache/
    Ignored:    analysis/ms14_lesions_cache/
    Ignored:    analysis/supp06_sccaf_cache/
    Ignored:    analysis/supp09_ancombc_cache/
    Ignored:    analysis/supp10_muscat_cache/
    Ignored:    analysis/supp10_muscat_heatmaps_cache/
    Ignored:    code/muscat_plan.txt
    Ignored:    data/
    Ignored:    figures/
    Ignored:    output/

Untracked files:
    Untracked:  analysis/supp10_muscat_heatmaps.Rmd
    Untracked:  analysis/temp_igll5.R
    Untracked:  asedrhg.png
    Untracked:  code/jobs/muscat_job_2021-06-17_broad.slurm
    Untracked:  code/jobs/muscat_job_2021-06-17_fine_gm.slurm
    Untracked:  code/jobs/muscat_job_2021-06-17_fine_wm.slurm
    Untracked:  code/supp09_ancombc.R

Unstaged changes:
    Modified:   analysis/ms10_muscat_template_broad.Rmd
    Modified:   analysis/ms10_muscat_template_fine.Rmd
    Modified:   analysis/ms12_markers.Rmd
    Modified:   analysis/ms14_lesions.Rmd
    Modified:   analysis/supp09_ancombc.Rmd
    Modified:   code/jobs/muscat_job_2021-06-05_broad.slurm
    Modified:   code/jobs/muscat_job_2021-06-05_fine_wm.slurm
    Modified:   code/ms09_ancombc.R
    Modified:   code/ms10_muscat_fns.R
    Modified:   code/ms10_muscat_runs.R
    Modified:   code/ms12_markers.R
    Modified:   code/ms14_lesions.R
    Deleted:    code/supp08_ancombc.R
    Modified:   code/supp10_muscat.R

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/ms10_muscat_template_broad.Rmd) and HTML (docs/ms10_muscat_template_broad.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	ac17711	Macnair	2021-06-15	Split top gene heatmaps by uniqueness
Rmd	b9b46aa	Macnair	2021-06-10	Fix mistake in logFC filtering
Rmd	8ccd4e7	Macnair	2021-06-08	Update muscat reports
Rmd	a58ad15	Macnair	2021-06-08	Update multiple aspects of muscat

What we did we do?

run_descs[run_tag]

$run10
[1] "lesions vs ctrl, GM, glmmtmb-nb, broad celltypes"

print(params)

$pb_f
[1] "output/ms07_soup/pb_sum_broad_2021-06-01.rds"

$subset_spec
$subset_spec$matter
[1] "GM"


$pb_soup_f
[1] "output/ms07_soup/pb_soup_broad_maximum_2021-06-01.rds"

$labels_f
[1] "data/byhand_markers/validation_markers_2021-05-31.csv"

$cluster_var
[1] "type_broad"

$formula_str
[1] "~ lesion_type + sex + age_norm + pmi_cat"

$padj_cut
[1] 0.05

$min_cells
[1] 10

$method_spec
$method_spec$method
[1] "glmmtmb-nb"

$method_spec$random_var
[1] "patient_id"


$filter
[1] "both"

$soup_cut
[1] 0.1

$paths_list
$paths_list$position
[1] "data/gmt_pathways/c1.all.v7.4.symbols.gmt"

$paths_list$curated
[1] "data/gmt_pathways/c2.all.v7.4.symbols.gmt"

$paths_list$mirs
[1] "data/gmt_pathways/c3.mir.v7.4.symbols.gmt"

$paths_list$TFs
[1] "data/gmt_pathways/c3.tft.v7.4.symbols.gmt"

$paths_list$go_bp
[1] "data/gmt_pathways/c5.go.bp.v7.4.symbols.gmt"

$paths_list$hpo
[1] "data/gmt_pathways/c5.hpo.v7.4.symbols.gmt"

$paths_list$immune
[1] "data/gmt_pathways/c7.immunesigdb.v7.4.symbols.gmt"

$paths_list$celltype
[1] "data/gmt_pathways/c8.all.v7.4.symbols.gmt"

$paths_list$hallmark
[1] "data/gmt_pathways/h.all.v7.4.symbols.gmt"


$n_cores
[1] 24

$output_fs
$output_fs$res_f
[1] "output/ms10_muscat/run10/muscat_res_run10_%s.rds"

$output_fs$res_dt_f
[1] "output/ms10_muscat/run10/muscat_res_dt_run10_%s.txt.gz"

$output_fs$ranef_dt_f
[1] "output/ms10_muscat/run10/muscat_ranef_dt_run10_%s.txt.gz"

$output_fs$fgsea_pat
[1] "output/ms10_muscat/run10/fgsea_dt_run10_%s_%s.txt.gz"

$output_fs$mds_dist_ls_f
[1] "output/ms10_muscat/run10/mds_dist_ls_run10_%s.rds"

$output_fs$mds_dist_f
[1] "output/ms10_muscat/run10/mds_dist_run10_%s.rds"

$output_fs$mds_all_f
[1] "output/ms10_muscat/run10/mds_all_dt_run10_%s.txt.gz"

$output_fs$mds_sep_f
[1] "output/ms10_muscat/run10/mds_sep_dt_run10_%s.txt.gz"

$output_fs$xl_f
[1] "output/ms10_muscat/run10/muscat_run10_%s.xlsx"

$output_fs$xl_wide_f
[1] "output/ms10_muscat/run10/muscat_wide_run10_%s.xlsx"

$output_fs$fgsea_xl_f
[1] "output/ms10_muscat/run10/muscat_GSEA_run10_%s.xlsx"

$output_fs$params_f
[1] "output/ms10_muscat/run10/muscat_params_run10_%s.rds"

$output_fs$log_f
[1] "output/ms10_muscat/run10/muscat_log_run10_%s.txt"


$call
run_muscat_and_gsea(run_tag = run_tag, pb_f = pb_f, subset_spec = subset_spec, 
    pb_soup_f = pb_soup_f, labels_f = labels_f, cluster_var = cluster_var, 
    labels_dt = labels_dt, formula_str = formula_str, padj_cut = padj_cut, 
    fgsea_cut = fgsea_cut, fc_cut = fc_cut, min_cells = min_cells, 
    method_spec = method_spec, filter = filter, soup_cut = soup_cut, 
    paths_list = paths_list, n_cores = n_cores, output_fs = output_fs)

$time_stamp
[1] "2021-06-17"

$fc_cut
[1] 1

Check sample design

plot_design_pca(pb, params$formula_str)