| ... | ... |
@@ -22,5 +22,13 @@ A data.frame to be used in \code{ComplexUpset::upset()}
|
| 22 | 22 |
Create a data frame that can be fed to the upset function |
| 23 | 23 |
} |
| 24 | 24 |
\examples{
|
| 25 |
-# TODO |
|
| 25 |
+# res_enrich object |
|
| 26 |
+data(res_enrich_macrophage, package = "GeneTonic") |
|
| 27 |
+res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive) |
|
| 28 |
+res_enrich <- get_aggrscores(res_enrich, res_de, anno_df) |
|
| 29 |
+ |
|
| 30 |
+create_upsetdata(res_enrich[1:20, ]) |
|
| 31 |
+dim(create_upsetdata(res_enrich[1:20, ])) |
|
| 32 |
+ |
|
| 33 |
+create_upsetdata(res_enrich[1:5, ], use_ids = TRUE) |
|
| 26 | 34 |
} |
| ... | ... |
@@ -6,7 +6,7 @@ |
| 6 | 6 |
\usage{
|
| 7 | 7 |
gs_upset( |
| 8 | 8 |
res_enrich, |
| 9 |
- res_de, |
|
| 9 |
+ res_de = NULL, |
|
| 10 | 10 |
annotation_obj = NULL, |
| 11 | 11 |
n_gs = 10, |
| 12 | 12 |
gtl = NULL, |
| ... | ... |
@@ -67,5 +67,53 @@ A \code{ggplot} object (if plotting), or alternatively a data.frame
|
| 67 | 67 |
Create an upset plot for genesets |
| 68 | 68 |
} |
| 69 | 69 |
\examples{
|
| 70 |
-# TODO |
|
| 70 |
+library("macrophage")
|
|
| 71 |
+library("DESeq2")
|
|
| 72 |
+library("org.Hs.eg.db")
|
|
| 73 |
+library("AnnotationDbi")
|
|
| 74 |
+ |
|
| 75 |
+# dds object |
|
| 76 |
+data("gse", package = "macrophage")
|
|
| 77 |
+dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition) |
|
| 78 |
+rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15) |
|
| 79 |
+dds_macrophage <- estimateSizeFactors(dds_macrophage) |
|
| 80 |
+ |
|
| 81 |
+# annotation object |
|
| 82 |
+anno_df <- data.frame( |
|
| 83 |
+ gene_id = rownames(dds_macrophage), |
|
| 84 |
+ gene_name = mapIds(org.Hs.eg.db, |
|
| 85 |
+ keys = rownames(dds_macrophage), |
|
| 86 |
+ column = "SYMBOL", |
|
| 87 |
+ keytype = "ENSEMBL" |
|
| 88 |
+ ), |
|
| 89 |
+ stringsAsFactors = FALSE, |
|
| 90 |
+ row.names = rownames(dds_macrophage) |
|
| 91 |
+) |
|
| 92 |
+ |
|
| 93 |
+# res object |
|
| 94 |
+data(res_de_macrophage, package = "GeneTonic") |
|
| 95 |
+res_de <- res_macrophage_IFNg_vs_naive |
|
| 96 |
+ |
|
| 97 |
+# res_enrich object |
|
| 98 |
+data(res_enrich_macrophage, package = "GeneTonic") |
|
| 99 |
+res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive) |
|
| 100 |
+res_enrich <- get_aggrscores(res_enrich, res_de, anno_df) |
|
| 101 |
+gs_upset(res_enrich, |
|
| 102 |
+ n_gs = 10) |
|
| 103 |
+ |
|
| 104 |
+gs_upset(res_enrich, res_de = res_de, annotation_obj = anno_df, |
|
| 105 |
+ n_gs = 8, |
|
| 106 |
+ add_de_direction = TRUE, add_de_gsgenes = TRUE) |
|
| 107 |
+ |
|
| 108 |
+# or using the practical gtl (GeneTonicList) |
|
| 109 |
+gtl_macrophage <- GeneTonic_list( |
|
| 110 |
+ dds = dds_macrophage, |
|
| 111 |
+ res_de = res_de, |
|
| 112 |
+ res_enrich = res_enrich, |
|
| 113 |
+ annotation_obj = anno_df |
|
| 114 |
+) |
|
| 115 |
+ |
|
| 116 |
+gs_upset(gtl = gtl_macrophage, |
|
| 117 |
+ n_gs = 15, |
|
| 118 |
+ add_de_direction = TRUE, add_de_gsgenes = TRUE) |
|
| 71 | 119 |
} |
