| ... | ... |
@@ -8,6 +8,7 @@ |
| 8 | 8 |
|
| 9 | 9 |
* Fixed the behavior of the reactive elements after uploading the `GeneTonicList` object at runtime. |
| 10 | 10 |
* Fixed the label namings for the `gs_heatmap` function |
| 11 |
+* The `enhance_table()` function can handle the case where a gene is in the enrichment results table but not present in the annotation (e.g. annotations are updated, so some correspondences might get lost). It also presents an informative message on which genesets/genes are potentially responsible for the behavior. |
|
| 11 | 12 |
|
| 12 | 13 |
# GeneTonic 2.0.0 |
| 13 | 14 |
|
| ... | ... |
@@ -94,18 +94,32 @@ enhance_table <- function(res_enrich, |
| 94 | 94 |
genes_thisset <- unlist(strsplit(genes_thisset, ",")) |
| 95 | 95 |
|
| 96 | 96 |
genesid_thisset <- annotation_obj$gene_id[match(genes_thisset, annotation_obj$gene_name)] |
| 97 |
- |
|
| 98 |
- res_thissubset <- res_de[genesid_thisset, ] |
|
| 97 |
+ |
|
| 98 |
+ # removing the genes not finding a match in the annotation |
|
| 99 |
+ no_anno_match <- is.na(genesid_thisset) |
|
| 100 |
+ genes_thisset_anno <- genes_thisset[!no_anno_match] |
|
| 101 |
+ genesid_thisset_anno <- genesid_thisset[!no_anno_match] |
|
| 102 |
+ # ... and informing on which genes might be troublesome |
|
| 103 |
+ if (any(no_anno_match)) {
|
|
| 104 |
+ message("Could not find a match in the annotation for some genes. ",
|
|
| 105 |
+ "Please inspect your results in detail for geneset ", |
|
| 106 |
+ gs, |
|
| 107 |
+ " the gene(s) named: ", |
|
| 108 |
+ paste0(genes_thisset[no_anno_match], collapse = ", ")) |
|
| 109 |
+ } |
|
| 110 |
+ |
|
| 111 |
+ res_thissubset <- res_de[genesid_thisset_anno, ] |
|
| 99 | 112 |
|
| 100 | 113 |
res_thissubset <- as.data.frame(res_thissubset) |
| 101 | 114 |
|
| 102 |
- res_thissubset$gene_name <- genes_thisset |
|
| 115 |
+ res_thissubset$gene_name <- genes_thisset_anno |
|
| 103 | 116 |
res_thissubset$gs_desc <- as.factor(res_enrich[gs, "gs_description"]) |
| 104 | 117 |
res_thissubset$gs_id <- res_enrich[gs, "gs_id"] |
| 105 | 118 |
# return(as.data.frame(res_thissubset)) |
| 106 | 119 |
return(res_thissubset) |
| 107 | 120 |
}) |
| 108 | 121 |
gs_fulllist <- do.call(rbind, gs_fulllist) |
| 122 |
+ # message(dim(gs_fulllist)[1]) |
|
| 109 | 123 |
|
| 110 | 124 |
this_contrast <- (sub(".*p-value: (.*)", "\\1", mcols(res_de, use.names = TRUE)["pvalue", "description"]))
|
| 111 | 125 |
|
| ... | ... |
@@ -28,14 +28,30 @@ test_that("Enhanced table is created", {
|
| 28 | 28 |
with_scores <- get_aggrscores(gtl = gtl_macrophage) |
| 29 | 29 |
expect_is(with_scores, "data.frame") |
| 30 | 30 |
|
| 31 |
- p2 <- enhance_table(res_enrich_IFNg_vs_naive, |
|
| 31 |
+ p2 <- enhance_table(with_scores, |
|
| 32 | 32 |
res_macrophage_IFNg_vs_naive, |
| 33 | 33 |
annotation_obj = anno_df, |
| 34 | 34 |
n_gs = 5, |
| 35 | 35 |
chars_limit = 60, |
| 36 |
- plot_title = "My custom title" |
|
| 36 |
+ plot_title = "My custom title - with scores" |
|
| 37 | 37 |
) |
| 38 | 38 |
expect_is(p2, "gg") |
| 39 |
+ |
|
| 40 |
+ re_modified <- res_enrich_IFNg_vs_naive |
|
| 41 |
+ # patching up some letters to mess up the name of a gene |
|
| 42 |
+ re_modified$gs_genes[1] <- |
|
| 43 |
+ paste0(re_modified$gs_genes[1], "AAAAAAAA") |
|
| 44 |
+ |
|
| 45 |
+ expect_message({
|
|
| 46 |
+ p3 <- enhance_table(re_modified, |
|
| 47 |
+ res_macrophage_IFNg_vs_naive, |
|
| 48 |
+ annotation_obj = anno_df, |
|
| 49 |
+ n_gs = 5, |
|
| 50 |
+ chars_limit = 60, |
|
| 51 |
+ plot_title = "After modifying the genes assigned to gs1" |
|
| 52 |
+ ) |
|
| 53 |
+ }) |
|
| 54 |
+ expect_is(p3, "gg") |
|
| 39 | 55 |
}) |
| 40 | 56 |
|
| 41 | 57 |
test_that("The distillery is up and running", {
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