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Enrichment for HCPC clusters inplemented
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,101 +1,103 @@ | ||
| --- | ||
| title: "ExpHunterSuite: Functional Report" | ||
| author: "SysBioLab" | ||
| output: | ||
| html_document: | ||
| toc: true | ||
| toc_float: true | ||
| df_print: paged | ||
| fig_width: 12 | ||
| --- | ||
|
|
||
| <style type='text/css'> | ||
| body .main-container { | ||
| max-width: 90%; | ||
|
|
||
| } | ||
|
|
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| .plot_real_size { | ||
| overflow: scroll; | ||
| max-height: 600px; | ||
| } | ||
|
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| .plot_real_size img{ | ||
| max-width: none; | ||
| max-height: none; | ||
| } | ||
|
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| embed { | ||
|
|
||
| } | ||
| </style> | ||
|
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| ```{r config, include=FALSE, message=FALSE} | ||
| require(ggplot2) | ||
| require(knitr) | ||
| require(clusterProfiler) | ||
| require(enrichplot) | ||
| require(DOSE) | ||
| ``` | ||
|
|
||
| ```{r child="func_initial_details.Rmd"} | ||
| ``` | ||
| ```{r child="func_deg_details.Rmd"} | ||
| ``` | ||
| ```{r child="func_top_genes.Rmd"} | ||
| ``` | ||
|
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||
|
|
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| ```{r ORA_analysis, echo=FALSE, results='asis', message=FALSE, warning=FALSE} | ||
| res_ora <- list() | ||
| for(funsys in names(flags_ora)) { | ||
| if(flags_ora[[funsys]] == TRUE) { | ||
| enrich_obj <- func_results$ORA[[funsys]] | ||
| exp_res <- knitr::knit_expand("ora_plots_all_objects.Rmd") | ||
| res_ora[[funsys]] <- knitr::knit(text=exp_res, quiet=TRUE) | ||
| } else { | ||
| res_ora[[funsys]] <- paste0("## **No ORA enrichment found for ", funsys, "**\n") | ||
| } | ||
| } | ||
| cat(unlist(res_ora), sep = '\n') | ||
| res_gsea <- list() | ||
| for(funsys in names(flags_gsea)) { | ||
| if(flags_gsea[[funsys]] == TRUE) { | ||
| enrich_obj <- func_results$GSEA[[funsys]] | ||
| exp_res <- knitr::knit_expand("gsea_plots_all_objects.Rmd") | ||
| res_gsea[[funsys]] <- knitr::knit(text=exp_res, quiet=TRUE) | ||
| } else { | ||
| res_gsea[[funsys]] <- paste0("## **No GSEA enrichment found for ", funsys, "**\n") | ||
| } | ||
| } | ||
| cat(unlist(res_gsea), sep = '\n') | ||
| ``` | ||
|
|
||
| ```{r PCA_enr, echo=FALSE, results='asis', message=FALSE, warning=FALSE} | ||
| res_PCA <- list() | ||
| for(funsys in names(flags_ora)) { | ||
| if (funsys %in% c("BP", "MF", "CC")){ | ||
| pca_enr_all <- func_results$PCA_enrichments$all_genes[[funsys]] | ||
| pca_enr_degs <- func_results$PCA_enrichments$DEGs[[funsys]] | ||
| pca_enr <- knitr::knit_expand("pca_enr.Rmd") | ||
| res_PCA[[funsys]] <- knitr::knit(text=pca_enr, quiet=TRUE) | ||
| } | ||
| } | ||
| cat(unlist(res_PCA), sep = '\n') | ||
| ``` | ||
|
|
||
| ## **Values of options passed to the Functional Hunter main function** | ||
| First column contains the option names; second column contains the given values for each option. | ||
| Note that large data objects (e.g. expression results, | ||
| organism table and custom annotation files) are not shown. | ||
| ```{r opt_vals, echo = FALSE, results='asis'} | ||
| final_main_params <- func_results$final_main_params[! sapply(func_results$final_main_params, is.list)] | ||
| print(knitr::kable(cbind(final_main_params))) | ||
| --- | ||
| title: "ExpHunterSuite: Functional Report" | ||
| author: "SysBioLab" | ||
| output: | ||
| html_document: | ||
| toc: true | ||
| toc_float: true | ||
| df_print: paged | ||
| fig_width: 12 | ||
| --- | ||
|
|
||
| <style type='text/css'> | ||
| body .main-container { | ||
| max-width: 90%; | ||
|
|
||
| } | ||
|
|
||
| .plot_real_size { | ||
| overflow: scroll; | ||
| max-height: 600px; | ||
| } | ||
|
|
||
| .plot_real_size img{ | ||
| max-width: none; | ||
| max-height: none; | ||
| } | ||
|
|
||
| embed { | ||
|
|
||
| } | ||
| </style> | ||
|
|
||
| ```{r config, include=FALSE, message=FALSE} | ||
| require(ggplot2) | ||
| require(knitr) | ||
| require(clusterProfiler) | ||
| require(enrichplot) | ||
| require(DOSE) | ||
| ``` | ||
|
|
||
| ```{r child="func_initial_details.Rmd"} | ||
| ``` | ||
| ```{r child="func_deg_details.Rmd"} | ||
| ``` | ||
| ```{r child="func_top_genes.Rmd"} | ||
| ``` | ||
|
|
||
|
|
||
| ```{r ORA_analysis, echo=FALSE, results='asis', message=FALSE, warning=FALSE} | ||
| res_ora <- list() | ||
| for(funsys in names(flags_ora)) { | ||
| if(flags_ora[[funsys]] == TRUE) { | ||
| enrich_obj <- func_results$ORA[[funsys]] | ||
| exp_res <- knitr::knit_expand("ora_plots_all_objects.Rmd") | ||
| res_ora[[funsys]] <- knitr::knit(text=exp_res, quiet=TRUE) | ||
| } else { | ||
| res_ora[[funsys]] <- paste0("## **No ORA enrichment found for ", funsys, "**\n") | ||
| } | ||
| } | ||
| cat(unlist(res_ora), sep = '\n') | ||
| res_gsea <- list() | ||
| for(funsys in names(flags_gsea)) { | ||
| if(flags_gsea[[funsys]] == TRUE) { | ||
| enrich_obj <- func_results$GSEA[[funsys]] | ||
| exp_res <- knitr::knit_expand("gsea_plots_all_objects.Rmd") | ||
| res_gsea[[funsys]] <- knitr::knit(text=exp_res, quiet=TRUE) | ||
| } else { | ||
| res_gsea[[funsys]] <- paste0("## **No GSEA enrichment found for ", funsys, "**\n") | ||
| } | ||
| } | ||
| cat(unlist(res_gsea), sep = '\n') | ||
| ``` | ||
|
|
||
| ```{r PCA_enr, echo=FALSE, results='asis', message=FALSE, warning=FALSE} | ||
| res_PCA <- list() | ||
| for(funsys in names(flags_ora)) { | ||
| if (funsys %in% c("BP", "MF", "CC")){ | ||
| pca_enr_all <- func_results$PCA_enrichments$all_genes[[funsys]] | ||
| pca_enr_degs <- func_results$PCA_enrichments$DEGs[[funsys]] | ||
| pca_cl_all <- func_results$PCA_clusters_results$all_genes[[funsys]] | ||
| pca_cl_degs <- func_results$PCA_clusters_results$DEGs[[funsys]] | ||
| pca_enr <- knitr::knit_expand("pca_enr.Rmd") | ||
| res_PCA[[funsys]] <- knitr::knit(text=pca_enr, quiet=TRUE) | ||
| } | ||
| } | ||
| cat(unlist(res_PCA), sep = '\n') | ||
| ``` | ||
|
|
||
| ## **Values of options passed to the Functional Hunter main function** | ||
| First column contains the option names; second column contains the given values for each option. | ||
| Note that large data objects (e.g. expression results, | ||
| organism table and custom annotation files) are not shown. | ||
| ```{r opt_vals, echo = FALSE, results='asis'} | ||
| final_main_params <- func_results$final_main_params[! sapply(func_results$final_main_params, is.list)] | ||
| print(knitr::kable(cbind(final_main_params))) | ||
| ``` |
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