Write vignette rough draft

[gabrielodom]

Draw from the vignettes at https://gabrielodom.github.io/pathwayPCA/articles/ to create a 50-minute long interactive presentation on pathwayPCA. Use this outline:

Activity	Time
Introduction to pathwayPCA	10m
Case Study 1: Estimating sample-specific pathway activities	10m
Case Study 2: Pathway analysis for multi-omics datasets	10m
Case Study 3: Analyzing experiments with covariates and interactions	10m
Summary and Conclusion	5m
Questions and Comments	5m

[gabrielodom]

I need help from @jamesban2015 for the biological motivation.

[gabrielodom]

@lxw391 comments:

1. SummarizedExperiment to tidy data
2. Explain that the samples for ovarian are from primary tumors (I had removed the "-01" from the sample ID)
3. Clean up (mostly remove) package library calls and descriptions
4. Remove the intercept term from the CoxPH hazard function (case study 3)

[gabrielodom]

@jamesban2015 comments:

1. For Figure 5.3.5, change "PC1 Value for Each Sample" to "PC1 Score for Each Sample"
2. Add label to Table 7.2: remind reader that these p-values are for the interaction term
3. For Figure 5.3.3, pathway label text far too small
4. Add the flowchart from the manuscript to section 4.2
5. @lizhongliu1996: update the Circos plot to include labels. Flip the colours (red > 0; blue < 0).

[gabrielodom]

@torongs82:

1. My presentation was not a workshop. Make sure to give users time to follow along with the code and execute it.
2. The ovCNV_df object has class spec_tbl_df in addition to its regular "tibble" classes.
3. The ovProteome_df object has data.frame only.

[gabrielodom]

COMPLETE:

1. Explain that the samples for ovarian are from primary tumors (I had removed the "-01" from the sample ID)
2. Clean up (mostly remove) package library calls and descriptions
3. Remove the intercept term from the CoxPH hazard function (case study 3)
4. For Figure 5.3.5, change "PC1 Value for Each Sample" to "PC1 Score for Each Sample"
5. Add label to Table 7.2: remind reader that these p-values are for the interaction term
6. For Figure 5.3.3, pathway label text far too small

[gabrielodom]

TO DO:

1. SummarizedExperiment to tidy data
2. Add the flowchart from the manuscript to section 4.2
3. The ovCNV_df object has class spec_tbl_df in addition to its regular "tibble" classes.
4. The kirpRNAseq_dfobject has class spec_tbl_df in addition to its regular "tibble" classes.
5. The ovProteome_df object has data.frame only.
6. Sort sections by "OPTIONAL" tags to ensure that people have time to follow and code along.