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add gsea plot functionality
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10adavis committed Dec 29, 2021
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<meta name="author" content="Andrew J. Davis, Ph.D." />

<meta name="date" content="2021-12-28" />
<meta name="date" content="2021-12-29" />

<title>Enter analysis name here</title>

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<h1 class="title toc-ignore">Enter analysis name here</h1>
<h4 class="author">Andrew J. Davis, Ph.D.</h4>
<h4 class="date">28 December 2021</h4>
<h4 class="date">29 December 2021</h4>

</div>

Expand Down Expand Up @@ -507,27 +507,17 @@ <h2>Mechanics:</h2>
<div id="output" class="section level2">
<h2>Output:</h2>
<p>The resulting output files were saved to the <a href="Results">Results</a> folder in this repository. Note that the contents of this folder will not be tracked by the remote repository by default (these files tend to be large to store on GitHub). To track the contents of this folder, one must remove the line “/Results/” from the <a href=".gitignore">.gitignore</a> file.</p>
<pre><code>#&gt; [1] &quot;1.03_Gather-and-Tidy-Data.html&quot;
#&gt; [2] &quot;2.03_DESeq2.html&quot;
#&gt; [3] &quot;2.07_Volcano-Plots.html&quot;
#&gt; [4] &quot;3.03_GSEA.html&quot;
#&gt; [5] &quot;4.03_Export-to-IPA.html&quot;
#&gt; [6] &quot;5.03_Gene-Heatmaps.html&quot;
#&gt; [7] &quot;anti_PDL_treated_tumor_vs_baseline_tumor_DESeq2.csv&quot;
#&gt; [8] &quot;anti_PDL_treated_tumor_vs_baseline_tumor_pvalue_histogram.tiff&quot;
#&gt; [9] &quot;anti_PDL_treated_tumor_vs_baseline_tumor_volcano_padj-0.1_log2FC-1.pdf&quot;
#&gt; [10] &quot;DEG_Summary_Table.csv&quot;
#&gt; [11] &quot;DESeq2_dispersions_plot.pdf&quot;
#&gt; [12] &quot;Filtered_Normalized_Counts.csv&quot;
#&gt; [13] &quot;Filtered_Raw_Counts.csv&quot;
#&gt; [14] &quot;GSEA_anti_PDL_treated_tumor_vs_baseline_tumor.csv&quot;
#&gt; [15] &quot;Heatmap_Select_Genes.pdf&quot;
#&gt; [16] &quot;PCA_PC1-vs-PC2_rlog_ellipses.tiff&quot;
#&gt; [17] &quot;PCA_PC1-vs-PC2_rlog.tiff&quot;
#&gt; [18] &quot;PCA_PC1-vs-PC2_VST_ellipses.tiff&quot;
#&gt; [19] &quot;PCA_PC1-vs-PC2_VST.tiff&quot;
#&gt; [20] &quot;Sample_Correlation_rlog.pdf&quot;
#&gt; [21] &quot;Sample_Correlation_VST.pdf&quot;</code></pre>
<pre><code>#&gt; [1] &quot;1.03_Gather-and-Tidy-Data.html&quot; &quot;2.03_DESeq2.html&quot;
#&gt; [3] &quot;2.07_Volcano-Plots.html&quot; &quot;3.03_GSEA.html&quot;
#&gt; [5] &quot;4.03_Export-to-IPA.html&quot; &quot;5.03_Gene-Heatmaps.html&quot;
#&gt; [7] &quot;anti_PDL_treated_tumor_vs_baseline_tumor_DESeq2.csv&quot; &quot;anti_PDL_treated_tumor_vs_baseline_tumor_pvalue_histogram.tiff&quot;
#&gt; [9] &quot;anti_PDL_treated_tumor_vs_baseline_tumor_volcano_padj-0.1_log2FC-1.pdf&quot; &quot;DEG_Summary_Table.csv&quot;
#&gt; [11] &quot;DESeq2_dispersions_plot.pdf&quot; &quot;Filtered_Normalized_Counts.csv&quot;
#&gt; [13] &quot;Filtered_Raw_Counts.csv&quot; &quot;GSEA_anti_PDL_treated_tumor_vs_baseline_tumor.csv&quot;
#&gt; [15] &quot;GSEA_Top-20-Gene-Sets_anti_PDL_treated_tumor_vs_baseline_tumor.pdf&quot; &quot;Heatmap_Select_Genes.pdf&quot;
#&gt; [17] &quot;PCA_PC1-vs-PC2_rlog_ellipses.tiff&quot; &quot;PCA_PC1-vs-PC2_rlog.tiff&quot;
#&gt; [19] &quot;PCA_PC1-vs-PC2_VST_ellipses.tiff&quot; &quot;PCA_PC1-vs-PC2_VST.tiff&quot;
#&gt; [21] &quot;Sample_Correlation_rlog.pdf&quot; &quot;Sample_Correlation_VST.pdf&quot;</code></pre>
</div>
<div id="ipa" class="section level2">
<h2>IPA:</h2>
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#&gt; LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
#&gt;
#&gt; locale:
#&gt; [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
#&gt; [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
#&gt; [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#&gt; [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#&gt; [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#&gt;
#&gt; attached base packages:
#&gt; [1] stats4 stats graphics grDevices datasets utils methods base
#&gt;
#&gt; other attached packages:
#&gt; [1] gitcreds_0.1.1 genefilter_1.76.0 gplots_3.1.1 msigdbr_7.4.1 biomartr_0.9.2
#&gt; [6] data.table_1.14.2 GSEABase_1.56.0 graph_1.72.0 annotate_1.72.0 XML_3.99-0.8
#&gt; [11] reactome.db_1.77.0 GO.db_3.14.0 fgsea_1.20.0 dplyr_1.0.7 rlist_0.4.6.2
#&gt; [16] pheatmap_1.0.12 org.Hs.eg.db_3.14.0 AnnotationDbi_1.56.2 readxl_1.3.1 ashr_2.2-47
#&gt; [21] DESeq2_1.34.0 SummarizedExperiment_1.24.0 Biobase_2.54.0 MatrixGenerics_1.6.0 matrixStats_0.61.0
#&gt; [26] GenomicRanges_1.46.1 GenomeInfoDb_1.30.0 IRanges_2.28.0 S4Vectors_0.32.3 BiocGenerics_0.40.0
#&gt; [31] rmarkdown_2.11 here_1.0.1 magrittr_2.0.1 EnhancedVolcano_1.12.0 ggrepel_0.9.1
#&gt; [36] ggplot2_3.3.5
#&gt; [1] genefilter_1.76.0 gplots_3.1.1 magrittr_2.0.1 EnhancedVolcano_1.12.0 ggrepel_0.9.1
#&gt; [6] rlist_0.4.6.2 pheatmap_1.0.12 ashr_2.2-47 DESeq2_1.34.0 SummarizedExperiment_1.24.0
#&gt; [11] MatrixGenerics_1.6.0 matrixStats_0.61.0 GenomicRanges_1.46.1 GenomeInfoDb_1.30.0 rmarkdown_2.11
#&gt; [16] here_1.0.1 msigdbr_7.4.1 biomartr_0.9.2 data.table_1.14.2 GSEABase_1.56.0
#&gt; [21] graph_1.72.0 annotate_1.72.0 XML_3.99-0.8 reactome.db_1.77.0 GO.db_3.14.0
#&gt; [26] org.Hs.eg.db_3.14.0 AnnotationDbi_1.56.2 IRanges_2.28.0 S4Vectors_0.32.3 Biobase_2.54.0
#&gt; [31] BiocGenerics_0.40.0 fgsea_1.20.0 dplyr_1.0.7 readxl_1.3.1 scales_1.1.1
#&gt; [36] RColorBrewer_1.1-2 ggplot2_3.3.5
#&gt;
#&gt; loaded via a namespace (and not attached):
#&gt; [1] fastmatch_1.1-3 BiocFileCache_2.2.0 splines_4.1.2 BiocParallel_1.28.3 digest_0.6.29 invgamma_1.1
#&gt; [7] htmltools_0.5.2 SQUAREM_2021.1 fansi_0.5.0 memoise_2.0.1 Biostrings_2.62.0 extrafont_0.17
#&gt; [13] extrafontdb_1.0 prettyunits_1.1.1 colorspace_2.0-2 blob_1.2.2 rappdirs_0.3.3 xfun_0.29
#&gt; [19] crayon_1.4.2 RCurl_1.98-1.5 survival_3.2-13 glue_1.6.0 gtable_0.3.0 zlibbioc_1.40.0
#&gt; [25] XVector_0.34.0 DelayedArray_0.20.0 proj4_1.0-10.1 Rttf2pt1_1.3.9 maps_3.4.0 scales_1.1.1
#&gt; [31] DBI_1.1.2 Rcpp_1.0.7 xtable_1.8-4 progress_1.2.2 bit_4.0.4 truncnorm_1.0-8
#&gt; [37] httr_1.4.2 RColorBrewer_1.1-2 ellipsis_0.3.2 pkgconfig_2.0.3 farver_2.1.0 dbplyr_2.1.1
#&gt; [43] locfit_1.5-9.4 utf8_1.2.2 tidyselect_1.1.1 labeling_0.4.2 rlang_0.4.12 munsell_0.5.0
#&gt; [49] cellranger_1.1.0 tools_4.1.2 cachem_1.0.6 cli_3.1.0 generics_0.1.1 RSQLite_2.2.9
#&gt; [55] evaluate_0.14 stringr_1.4.0 fastmap_1.1.0 yaml_2.2.1 babelgene_21.4 knitr_1.37
#&gt; [61] bit64_4.0.5 caTools_1.18.2 purrr_0.3.4 KEGGREST_1.34.0 ash_1.0-15 ggrastr_1.0.1
#&gt; [67] xml2_1.3.3 biomaRt_2.50.1 compiler_4.1.2 beeswarm_0.4.0 filelock_1.0.2 curl_4.3.2
#&gt; [73] png_0.1-7 tibble_3.1.6 geneplotter_1.72.0 stringi_1.7.6 highr_0.9 ggalt_0.4.0
#&gt; [79] lattice_0.20-45 Matrix_1.4-0 vctrs_0.3.8 pillar_1.6.4 lifecycle_1.0.1 BiocManager_1.30.16
#&gt; [85] jquerylib_0.1.4 bitops_1.0-7 irlba_2.3.5 R6_2.5.1 renv_0.14.0 KernSmooth_2.23-20
#&gt; [91] gridExtra_2.3 vipor_0.4.5 MASS_7.3-54 gtools_3.9.2 assertthat_0.2.1 rprojroot_2.0.2
#&gt; [97] withr_2.4.3 GenomeInfoDbData_1.2.7 parallel_4.1.2 hms_1.1.1 grid_4.1.2 mixsqp_0.3-43
#&gt; [103] ggbeeswarm_0.6.0</code></pre>
<p>This document was processed on: 2021-12-28.</p>
#&gt; [1] fastmatch_1.1-3 BiocFileCache_2.2.0 splines_4.1.2 BiocParallel_1.28.3 digest_0.6.29 invgamma_1.1 htmltools_0.5.2
#&gt; [8] SQUAREM_2021.1 fansi_0.5.0 memoise_2.0.1 Biostrings_2.62.0 extrafont_0.17 extrafontdb_1.0 prettyunits_1.1.1
#&gt; [15] colorspace_2.0-2 blob_1.2.2 rappdirs_0.3.3 xfun_0.29 crayon_1.4.2 RCurl_1.98-1.5 survival_3.2-13
#&gt; [22] glue_1.6.0 gtable_0.3.0 zlibbioc_1.40.0 XVector_0.34.0 DelayedArray_0.20.0 proj4_1.0-10.1 Rttf2pt1_1.3.9
#&gt; [29] maps_3.4.0 DBI_1.1.2 Rcpp_1.0.7 xtable_1.8-4 progress_1.2.2 bit_4.0.4 truncnorm_1.0-8
#&gt; [36] httr_1.4.2 ellipsis_0.3.2 pkgconfig_2.0.3 farver_2.1.0 dbplyr_2.1.1 locfit_1.5-9.4 utf8_1.2.2
#&gt; [43] tidyselect_1.1.1 labeling_0.4.2 rlang_0.4.12 munsell_0.5.0 cellranger_1.1.0 tools_4.1.2 cachem_1.0.6
#&gt; [50] cli_3.1.0 generics_0.1.1 RSQLite_2.2.9 evaluate_0.14 stringr_1.4.0 fastmap_1.1.0 yaml_2.2.1
#&gt; [57] babelgene_21.4 knitr_1.37 bit64_4.0.5 caTools_1.18.2 purrr_0.3.4 KEGGREST_1.34.0 ash_1.0-15
#&gt; [64] ggrastr_1.0.1 xml2_1.3.3 biomaRt_2.50.1 compiler_4.1.2 beeswarm_0.4.0 filelock_1.0.2 curl_4.3.2
#&gt; [71] png_0.1-7 tibble_3.1.6 geneplotter_1.72.0 stringi_1.7.6 highr_0.9 ggalt_0.4.0 lattice_0.20-45
#&gt; [78] Matrix_1.4-0 vctrs_0.3.8 pillar_1.6.4 lifecycle_1.0.1 BiocManager_1.30.16 jquerylib_0.1.4 bitops_1.0-7
#&gt; [85] irlba_2.3.5 R6_2.5.1 renv_0.14.0 KernSmooth_2.23-20 gridExtra_2.3 vipor_0.4.5 MASS_7.3-54
#&gt; [92] gtools_3.9.2 assertthat_0.2.1 rprojroot_2.0.2 withr_2.4.3 GenomeInfoDbData_1.2.7 parallel_4.1.2 hms_1.1.1
#&gt; [99] grid_4.1.2 mixsqp_0.3-43 tinytex_0.36 ggbeeswarm_0.6.0</code></pre>
<p>This document was processed on: 2021-12-29.</p>
</div>
</div>

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