Last updated: 2024-01-15

Checks: 2 0

Knit directory: mi_spatialomics/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). 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: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Repository version: 51d8b3b

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 51d8b3b. 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:    .Rproj.user/
    Ignored:    analysis/.DS_Store
    Ignored:    analysis/.Rhistory
    Ignored:    analysis/deprecated/.DS_Store
    Ignored:    analysis/molecular_cartography_python/.DS_Store
    Ignored:    analysis/molecular_cartography_python/figures/
    Ignored:    analysis/seqIF_python/.DS_Store
    Ignored:    data/.DS_Store
    Ignored:    data/140623.calcagno_et_al.seurat_object.rds
    Ignored:    data/Calcagno2022_int_logNorm_annot.h5Seurat
    Ignored:    data/pixie.cell_table_size_normalized_cell_labels.csv
    Ignored:    data/results_cts_100.sqm
    Ignored:    data/seqIF_regions_annotations/
    Ignored:    data/seurat/
    Ignored:    figures/.DS_Store
    Ignored:    figures/Figure_5.pathway_plot.pdf
    Ignored:    figures/Figure_5.pca_plot.pdf
    Ignored:    figures/Figure_5.pca_plot.png
    Ignored:    figures/Figure_5.volcano_plot.pdf
    Ignored:    figures/Figure_5.vwf_expression_plot.pdf
    Ignored:    figures/Figure_5.vwf_specificity_plot.pdf
    Ignored:    figures/Supplementary_figure_3.segmentation_metrics.eps
    Ignored:    figures/Supplementary_figure_3.segmentation_metrics.png
    Ignored:    figures/figures.supplementary_figure4.png
    Ignored:    figures/mol_cart.Figure_2.gains.pdf
    Ignored:    figures/mol_cart.Figure_2.misty_gains.pdf
    Ignored:    figures/mol_cart.Myeloid_distribution.png
    Ignored:    figures/mol_cart.Nppa_distribution.eps
    Ignored:    figures/mol_cart.Nppa_distribution.pdf
    Ignored:    figures/mol_cart.Nppa_distribution.png
    Ignored:    figures/supplementary_figure4.cell_type_distributions.eps
    Ignored:    figures/supplementary_figure4.cell_type_distributions.png
    Ignored:    output/.DS_Store
    Ignored:    output/mol_cart.harmony_object.h5Seurat
    Ignored:    output/molkart/
    Ignored:    output/proteomics/
    Ignored:    output/seqIF/
    Ignored:    output/tx_abundances_per_slide.tsv
    Ignored:    pipeline_configs/mcmicro/
    Ignored:    plots/.DS_Store
    Ignored:    plots/Figure1.umap_plot.pdf
    Ignored:    plots/Figure3.ccr2_monomacro_regions.pdf
    Ignored:    plots/Figure3.cell_types_overtimes.pdf
    Ignored:    plots/Figure3.pixel_clusters_overtimes.pdf
    Ignored:    plots/mol_cart.Figure_2.ct_percentage.pdf
    Ignored:    plots/molkart.squidpy.co_occurrence_plot.CMs_Nppa.sample_2d_r1_s1.png
    Ignored:    plots/molkart.squidpy.co_occurrence_plot.CMs_Nppa.sample_2d_r2_s1.png
    Ignored:    plots/molkart.squidpy.co_occurrence_plot.CMs_Nppa.sample_control_r1_s1.png
    Ignored:    plots/molkart.squidpy.co_occurrence_plot.CMs_Nppa.sample_control_r2_s1.png
    Ignored:    plots/molkart.squidpy.co_occurrence_plot.Endocardial_cells.sample_2d_r1_s1.png
    Ignored:    plots/molkart.squidpy.co_occurrence_plot.Endocardial_cells.sample_2d_r2_s1.png
    Ignored:    plots/molkart.squidpy.co_occurrence_plot.Endocardial_cells.sample_control_r1_s1.png
    Ignored:    plots/molkart.squidpy.co_occurrence_plot.Endocardial_cells.sample_control_r2_s1.png
    Ignored:    plots/molkart.squidpy.co_occurrence_plot.Myeloid_cells.sample_2d_r1_s1.png
    Ignored:    plots/molkart.squidpy.co_occurrence_plot.Myeloid_cells.sample_2d_r2_s1.png
    Ignored:    plots/molkart.squidpy.co_occurrence_plot.Myeloid_cells.sample_control_r1_s1.png
    Ignored:    plots/molkart.squidpy.co_occurrence_plot.Myeloid_cells.sample_control_r2_s1.png
    Ignored:    plots/molkart.squidpy.nhood_enrichment_plot.sample_2d_r1_s1.png
    Ignored:    plots/molkart.squidpy.nhood_enrichment_plot.sample_2d_r2_s1.png
    Ignored:    plots/molkart.squidpy.nhood_enrichment_plot.sample_control_r1_s1.png
    Ignored:    plots/molkart.squidpy.nhood_enrichment_plot.sample_control_r2_s1.png
    Ignored:    references/.DS_Store
    Ignored:    renv/library/
    Ignored:    renv/staging/

Untracked files:
    Untracked:  analysis/mistyfy.R
    Untracked:  analysis/molecular_cartography_python/molkart.count_spots_on_tissue.ipynb
    Untracked:  analysis/molecular_cartography_python/molkart.scanpy_analysis.ipynb
    Untracked:  analysis/molkart.QC_spots.Rmd
    Untracked:  analysis/molkart.misty_analysis.Rmd
    Untracked:  annotations/
    Untracked:  references/molkart.image_dimensions.csv
    Untracked:  sample_2d_r1_s1/
    Untracked:  sample_4h_r1_s1/

Unstaged changes:
    Modified:   analysis/data_processing.Rmd
    Modified:   analysis/figures.supplementary_figure_2.Rmd
    Deleted:    analysis/mol_cart.QC_spots.Rmd
    Deleted:    analysis/molecular_cartography_python/mol_cart.count_spots_on_tissue.ipynb
    Modified:   analysis/molecular_cartography_python/molkart.local_analysis_lianaplus.ipynb
    Modified:   analysis/molkart.seurat_analysis.Rmd
    Modified:   figures/Supplementary_figure_2.eps
    Modified:   figures/Supplementary_figure_2.png
    Modified:   plots/molkart.umap_time.png

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/data_analysis.Rmd) and HTML (docs/data_analysis.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 51d8b3b FloWuenne 2024-01-15 wflow_publish("./analysis/data_analysis.Rmd")
Rmd 2d9b909 FloWuenne 2024-01-09 Pushing latest changes. Updating molkart data.
html 2d9b909 FloWuenne 2024-01-09 Pushing latest changes. Updating molkart data.
html 2dcd178 FloWuenne 2023-12-06 wflow_publish("*")
Rmd 5dee03d FloWuenne 2023-09-04 Latest code update.
html 5dee03d FloWuenne 2023-09-04 Latest code update.
html d7ea71e FloWuenne 2023-08-11 Build site.
Rmd 64318a3 FloWuenne 2023-08-11 wflow_publish(c("analysis/molkart.process_quantifications_seurat.Rmd",
Rmd 9b98d64 FloWuenne 2023-08-04 Updated python and R scripts for Molkart.
html 67e546d FloWuenne 2023-07-23 Build site.
Rmd ed31d81 FloWuenne 2023-07-02 Finalized proteomics analysis.
html ed31d81 FloWuenne 2023-07-02 Finalized proteomics analysis.
html c1395e6 FloWuenne 2023-06-20 Build site.
Rmd 236130c FloWuenne 2023-06-20 Updating proteomic analysis.
html 236130c FloWuenne 2023-06-20 Updating proteomic analysis.
html 05aec09 FloWuenne 2023-06-14 Build site.
Rmd 0eba381 FloWuenne 2023-06-14 Updating Data analysis links.
html 0eba381 FloWuenne 2023-06-14 Updating Data analysis links.
html f412578 FloWuenne 2023-06-14 Build site.
Rmd 2d015dd FloWuenne 2023-06-14 Finalized imputation with RF.
html 2d015dd FloWuenne 2023-06-14 Finalized imputation with RF.
html 5816aca FloWuenne 2023-06-12 Build site.
Rmd 3b5ca40 FloWuenne 2023-06-12 Added code for supplementary Figures.
html 3b5ca40 FloWuenne 2023-06-12 Added code for supplementary Figures.
html e3bbd70 FloWuenne 2023-06-12 Build site.
Rmd 412d64f FloWuenne 2023-06-12 Fixed links in data_analysis
html 9603ecd FloWuenne 2023-06-12 Build site.
Rmd ff0c849 FloWuenne 2023-06-12 wflow_publish("*")
html 700ba8c FloWuenne 2023-06-12 Build site.
Rmd ebb85a5 FloWuenne 2023-06-12 Updated organization for proteomics data analysis.
html 51754b9 FloWuenne 2023-06-12 Build site.
html d764fa8 FloWuenne 2023-06-12 Build site.
Rmd 62020bf FloWuenne 2023-06-12 Configure site header.

Molecular Cartography

These scripts were used to analyze Molecular Cartography data following processing with the nf-Molkart pipeline.