... | ... |
@@ -30,7 +30,7 @@ NULL |
30 | 30 |
#' |
31 | 31 |
#' Details on how this object has been created are included in the `create_gt_data.R` |
32 | 32 |
#' script, included in the `scripts` folder of the `GeneTonic` package. |
33 |
-#' |
|
33 |
+#' |
|
34 | 34 |
#' @family pathway-analysis-results |
35 | 35 |
#' |
36 | 36 |
#' @references Alasoo, et al. "Shared genetic effects on chromatin and gene |
... | ... |
@@ -54,7 +54,7 @@ NULL |
54 | 54 |
#' |
55 | 55 |
#' Details on how this object has been created are included in the `create_gt_data.R` |
56 | 56 |
#' script, included in the `scripts` folder of the `GeneTonic` package. |
57 |
-#' |
|
57 |
+#' |
|
58 | 58 |
#' @family pathway-analysis-results |
59 | 59 |
#' |
60 | 60 |
#' @references Alasoo, et al. "Shared genetic effects on chromatin and gene |
... | ... |
@@ -79,7 +79,7 @@ NULL |
79 | 79 |
#' |
80 | 80 |
#' Details on how this object has been created are included in the `create_gt_data.R` |
81 | 81 |
#' script, included in the `scripts` folder of the `GeneTonic` package. |
82 |
-#' |
|
82 |
+#' |
|
83 | 83 |
#' @family pathway-analysis-results |
84 | 84 |
#' |
85 | 85 |
#' @references Alasoo, et al. "Shared genetic effects on chromatin and gene |
... | ... |
@@ -111,6 +111,3 @@ NULL |
111 | 111 |
#' @name fgseaRes |
112 | 112 |
#' @docType data |
113 | 113 |
NULL |
114 |
- |
|
115 |
- |
|
116 |
- |
... | ... |
@@ -44,7 +44,7 @@ |
44 | 44 |
#' |
45 | 45 |
#' # dds object |
46 | 46 |
#' data("gse", package = "macrophage") |
47 |
-#' dds_macrophage <- DESeqDataSet(gse, design = ~line + condition) |
|
47 |
+#' dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition) |
|
48 | 48 |
#' rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15) |
49 | 49 |
#' dds_macrophage <- estimateSizeFactors(dds_macrophage) |
50 | 50 |
#' |
... | ... |
@@ -52,9 +52,10 @@ |
52 | 52 |
#' anno_df <- data.frame( |
53 | 53 |
#' gene_id = rownames(dds_macrophage), |
54 | 54 |
#' gene_name = mapIds(org.Hs.eg.db, |
55 |
-#' keys = rownames(dds_macrophage), |
|
56 |
-#' column = "SYMBOL", |
|
57 |
-#' keytype = "ENSEMBL"), |
|
55 |
+#' keys = rownames(dds_macrophage), |
|
56 |
+#' column = "SYMBOL", |
|
57 |
+#' keytype = "ENSEMBL" |
|
58 |
+#' ), |
|
58 | 59 |
#' stringsAsFactors = FALSE, |
59 | 60 |
#' row.names = rownames(dds_macrophage) |
60 | 61 |
#' ) |
... | ... |
@@ -77,22 +78,26 @@ |
77 | 78 |
#' ) |
78 | 79 |
#' |
79 | 80 |
#' # now everything is in place to launch the app |
80 |
-#' if (interactive()) |
|
81 |
+#' if (interactive()) { |
|
81 | 82 |
#' GeneTonic(gtl = gtl_macrophage) |
83 |
+#' } |
|
82 | 84 |
GeneTonic_list <- function(dds, |
83 |
- res_de, |
|
84 |
- res_enrich, |
|
85 |
- annotation_obj) { |
|
86 |
- |
|
87 |
- checkup_GeneTonic(dds, |
|
88 |
- res_de, |
|
89 |
- res_enrich, |
|
90 |
- annotation_obj) |
|
85 |
+ res_de, |
|
86 |
+ res_enrich, |
|
87 |
+ annotation_obj) { |
|
88 |
+ checkup_GeneTonic( |
|
89 |
+ dds, |
|
90 |
+ res_de, |
|
91 |
+ res_enrich, |
|
92 |
+ annotation_obj |
|
93 |
+ ) |
|
91 | 94 |
|
92 |
- gtl <- list(dds = dds, |
|
93 |
- res_de = res_de, |
|
94 |
- res_enrich = res_enrich, |
|
95 |
- annotation_obj = annotation_obj) |
|
95 |
+ gtl <- list( |
|
96 |
+ dds = dds, |
|
97 |
+ res_de = res_de, |
|
98 |
+ res_enrich = res_enrich, |
|
99 |
+ annotation_obj = annotation_obj |
|
100 |
+ ) |
|
96 | 101 |
|
97 | 102 |
describe_gtl(gtl) |
98 | 103 |
|
... | ... |
@@ -111,7 +116,6 @@ GeneTonic_list <- function(dds, |
111 | 116 |
#' @return Invisible NULL - the information is displayed as a message in the |
112 | 117 |
#' console |
113 | 118 |
describe_gtl <- function(gtl) { |
114 |
- |
|
115 | 119 |
dds <- gtl$dds |
116 | 120 |
res_de <- gtl$res_de |
117 | 121 |
res_enrich <- gtl$res_enrich |
... | ... |
@@ -138,12 +142,15 @@ describe_gtl <- function(gtl) { |
138 | 142 |
message( |
139 | 143 |
sprintf( |
140 | 144 |
"Providing an expression object (as DESeqDataset) of %d features over %d samples", |
141 |
- n_features, n_samples) |
|
145 |
+ n_features, n_samples |
|
146 |
+ ) |
|
142 | 147 |
) |
143 | 148 |
message("\n----- res_de object -----") |
144 | 149 |
message( |
145 |
- sprintf("Providing a DE result object (as DESeqResults), %d features tested, %d found as DE", |
|
146 |
- n_tested, n_DE) |
|
150 |
+ sprintf( |
|
151 |
+ "Providing a DE result object (as DESeqResults), %d features tested, %d found as DE", |
|
152 |
+ n_tested, n_DE |
|
153 |
+ ) |
|
147 | 154 |
) |
148 | 155 |
message(sprintf("Upregulated: %d", n_upDE)) |
149 | 156 |
message(sprintf("Downregulated: %d", n_downDE)) |
... | ... |
@@ -158,7 +165,8 @@ describe_gtl <- function(gtl) { |
158 | 165 |
message( |
159 | 166 |
sprintf( |
160 | 167 |
"Providing an annotation object of %d features with information on %d identifier types", |
161 |
- n_featanno, n_featids) |
|
168 |
+ n_featanno, n_featids |
|
169 |
+ ) |
|
162 | 170 |
) |
163 | 171 |
|
164 | 172 |
return(invisible(NULL)) |
... | ... |
@@ -202,7 +210,8 @@ go_2_html <- function(go_id, |
202 | 210 |
lapply(Synonym(fullinfo), function(arg) { |
203 | 211 |
paste0(tags$b("Synonym: "), arg, tags$br()) |
204 | 212 |
}) |
205 |
- ), collapse = "" |
|
213 |
+ ), |
|
214 |
+ collapse = "" |
|
206 | 215 |
) |
207 | 216 |
go_secondary <- Secondary(fullinfo) |
208 | 217 |
if (!is.null(res_enrich)) { |
... | ... |
@@ -225,9 +234,10 @@ go_2_html <- function(go_id, |
225 | 234 |
ifelse( |
226 | 235 |
!is.null(res_enrich), |
227 | 236 |
paste0(tags$b("p-value: "), go_pvalue, tags$br(), |
228 |
- tags$b("Z-score: "), go_zscore, tags$br(), |
|
229 |
- tags$b("Aggregated score: "), go_aggrscore, tags$br(), |
|
230 |
- collapse = ""), |
|
237 |
+ tags$b("Z-score: "), go_zscore, tags$br(), |
|
238 |
+ tags$b("Aggregated score: "), go_aggrscore, tags$br(), |
|
239 |
+ collapse = "" |
|
240 |
+ ), |
|
231 | 241 |
"" |
232 | 242 |
), |
233 | 243 |
tags$b("Ontology: "), go_ontology, tags$br(), tags$br(), |
... | ... |
@@ -236,7 +246,8 @@ go_2_html <- function(go_id, |
236 | 246 |
ifelse( |
237 | 247 |
length(go_secondary) > 0, |
238 | 248 |
paste0(tags$b("Secondary: "), go_secondary, collapse = ""), |
239 |
- "") |
|
249 |
+ "" |
|
250 |
+ ) |
|
240 | 251 |
) |
241 | 252 |
return(HTML(mycontent)) |
242 | 253 |
} |
... | ... |
@@ -248,10 +259,12 @@ go_2_html <- function(go_id, |
248 | 259 |
#' @return HTML for an action button |
249 | 260 |
#' @noRd |
250 | 261 |
.link2amigo <- function(val) { |
251 |
- sprintf('<a href = "http://amigo.geneontology.org/amigo/term/%s" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>', |
|
252 |
- val, |
|
253 |
- .actionbutton_biocstyle, |
|
254 |
- val) |
|
262 |
+ sprintf( |
|
263 |
+ '<a href = "http://amigo.geneontology.org/amigo/term/%s" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>', |
|
264 |
+ val, |
|
265 |
+ .actionbutton_biocstyle, |
|
266 |
+ val |
|
267 |
+ ) |
|
255 | 268 |
} |
256 | 269 |
|
257 | 270 |
#' Information on a gene |
... | ... |
@@ -284,9 +297,11 @@ geneinfo_2_html <- function(gene_id, |
284 | 297 |
if (!is.null(res_de)) { |
285 | 298 |
gid <- match(gene_id, res_de$SYMBOL) |
286 | 299 |
if (is.na(gid)) { |
287 |
- message("Could not find the specified gene (`", gene_id, |
|
288 |
- "`) in the `res_de` object. \n", |
|
289 |
- "Still, the general HTML content has been generated.") |
|
300 |
+ message( |
|
301 |
+ "Could not find the specified gene (`", gene_id, |
|
302 |
+ "`) in the `res_de` object. \n", |
|
303 |
+ "Still, the general HTML content has been generated." |
|
304 |
+ ) |
|
290 | 305 |
gene_adjpvalue <- tags$em("not found") |
291 | 306 |
gene_logfc <- tags$em("not found") |
292 | 307 |
} else { |
... | ... |
@@ -303,8 +318,9 @@ geneinfo_2_html <- function(gene_id, |
303 | 318 |
ifelse( |
304 | 319 |
!is.null(res_de), |
305 | 320 |
paste0(tags$b("DE p-value (adjusted): "), gene_adjpvalue, tags$br(), |
306 |
- tags$b("DE log2FoldChange: "), gene_logfc, |
|
307 |
- collapse = ""), |
|
321 |
+ tags$b("DE log2FoldChange: "), gene_logfc, |
|
322 |
+ collapse = "" |
|
323 |
+ ), |
|
308 | 324 |
"" |
309 | 325 |
) |
310 | 326 |
) |
... | ... |
@@ -318,10 +334,12 @@ geneinfo_2_html <- function(gene_id, |
318 | 334 |
#' @return HTML for an action button |
319 | 335 |
#' @noRd |
320 | 336 |
.link2ncbi <- function(val) { |
321 |
- sprintf('<a href = "http://www.ncbi.nlm.nih.gov/gene/?term=%s[sym]" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>', |
|
322 |
- val, |
|
323 |
- .actionbutton_biocstyle, |
|
324 |
- val) |
|
337 |
+ sprintf( |
|
338 |
+ '<a href = "http://www.ncbi.nlm.nih.gov/gene/?term=%s[sym]" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>', |
|
339 |
+ val, |
|
340 |
+ .actionbutton_biocstyle, |
|
341 |
+ val |
|
342 |
+ ) |
|
325 | 343 |
} |
326 | 344 |
|
327 | 345 |
#' Link to the GeneCards database |
... | ... |
@@ -331,10 +349,12 @@ geneinfo_2_html <- function(gene_id, |
331 | 349 |
#' @return HTML for an action button |
332 | 350 |
#' @noRd |
333 | 351 |
.link2genecards <- function(val) { |
334 |
- sprintf('<a href = "https://www.genecards.org/cgi-bin/carddisp.pl?gene=%s" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>', |
|
335 |
- val, |
|
336 |
- .actionbutton_biocstyle, |
|
337 |
- val) |
|
352 |
+ sprintf( |
|
353 |
+ '<a href = "https://www.genecards.org/cgi-bin/carddisp.pl?gene=%s" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>', |
|
354 |
+ val, |
|
355 |
+ .actionbutton_biocstyle, |
|
356 |
+ val |
|
357 |
+ ) |
|
338 | 358 |
} |
339 | 359 |
|
340 | 360 |
#' Link to the GTEx Portal |
... | ... |
@@ -344,10 +364,12 @@ geneinfo_2_html <- function(gene_id, |
344 | 364 |
#' @return HTML for an action button |
345 | 365 |
#' @noRd |
346 | 366 |
.link2gtex <- function(val) { |
347 |
- sprintf('<a href = "https://www.gtexportal.org/home/gene/%s" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-dna"></i>%s</a>', |
|
348 |
- val, |
|
349 |
- .actionbutton_biocstyle, |
|
350 |
- val) |
|
367 |
+ sprintf( |
|
368 |
+ '<a href = "https://www.gtexportal.org/home/gene/%s" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-dna"></i>%s</a>', |
|
369 |
+ val, |
|
370 |
+ .actionbutton_biocstyle, |
|
371 |
+ val |
|
372 |
+ ) |
|
351 | 373 |
} |
352 | 374 |
|
353 | 375 |
|
... | ... |
@@ -365,19 +387,23 @@ generate_buttons_hubgenes <- function(x) { |
365 | 387 |
'<a href = "http://www.ncbi.nlm.nih.gov/gene/?term=%s[sym]" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>', |
366 | 388 |
x, |
367 | 389 |
.actionbutton_biocstyle, |
368 |
- "NCBI"), |
|
390 |
+ "NCBI" |
|
391 |
+ ), |
|
369 | 392 |
sprintf( |
370 | 393 |
'<a href = "https://www.genecards.org/cgi-bin/carddisp.pl?gene=%s" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>', |
371 | 394 |
x, |
372 | 395 |
.actionbutton_biocstyle, |
373 |
- "GeneCards"), |
|
396 |
+ "GeneCards" |
|
397 |
+ ), |
|
374 | 398 |
sprintf( |
375 | 399 |
'<a href = "https://www.gtexportal.org/home/gene/%s" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>', |
376 | 400 |
x, |
377 | 401 |
.actionbutton_biocstyle, |
378 |
- "GTEx"), |
|
379 |
- tags$br(style="display:inline-block"), |
|
380 |
- collapse = "\t") |
|
402 |
+ "GTEx" |
|
403 |
+ ), |
|
404 |
+ tags$br(style = "display:inline-block"), |
|
405 |
+ collapse = "\t" |
|
406 |
+ ) |
|
381 | 407 |
return(mybuttons) |
382 | 408 |
} |
383 | 409 |
|
... | ... |
@@ -399,7 +425,7 @@ generate_buttons_hubgenes <- function(x) { |
399 | 425 |
#' @examples |
400 | 426 |
#' a <- seq(1, 21, 2) |
401 | 427 |
#' b <- seq(1, 11, 2) |
402 |
-#' overlap_coefficient(a,b) |
|
428 |
+#' overlap_coefficient(a, b) |
|
403 | 429 |
overlap_coefficient <- function(x, y) { |
404 | 430 |
length(intersect(x, y)) / min(length(x), length(y)) |
405 | 431 |
} |
... | ... |
@@ -417,7 +443,7 @@ overlap_coefficient <- function(x, y) { |
417 | 443 |
#' @examples |
418 | 444 |
#' a <- seq(1, 21, 2) |
419 | 445 |
#' b <- seq(1, 11, 2) |
420 |
-#' overlap_jaccard_index(a,b) |
|
446 |
+#' overlap_jaccard_index(a, b) |
|
421 | 447 |
overlap_jaccard_index <- function(x, y) { |
422 | 448 |
length(intersect(x, y)) / length(unique(c(x, y))) |
423 | 449 |
# about 2x faster than using union() |
... | ... |
@@ -463,20 +489,22 @@ overlap_jaccard_index <- function(x, y) { |
463 | 489 |
#' res_df <- deseqresult2df(res_macrophage_IFNg_vs_naive) |
464 | 490 |
#' library("magrittr") |
465 | 491 |
#' library("DT") |
466 |
-#' DT::datatable(res_df [1:50, ], |
|
467 |
-#' options = list( |
|
468 |
-#' pageLength = 25, |
|
469 |
-#' columnDefs = list( |
|
470 |
-#' list(className = "dt-center", targets = "_all") |
|
471 |
-#' ) |
|
472 |
-#' ) |
|
492 |
+#' DT::datatable(res_df[1:50, ], |
|
493 |
+#' options = list( |
|
494 |
+#' pageLength = 25, |
|
495 |
+#' columnDefs = list( |
|
496 |
+#' list(className = "dt-center", targets = "_all") |
|
497 |
+#' ) |
|
498 |
+#' ) |
|
473 | 499 |
#' ) %>% |
474 | 500 |
#' formatRound(columns = c("log2FoldChange"), digits = 3) %>% |
475 | 501 |
#' formatStyle( |
476 | 502 |
#' "log2FoldChange", |
477 |
-#' background = styleColorBar_divergent(res_df$log2FoldChange, |
|
478 |
-#' scales::alpha("navyblue", 0.4), |
|
479 |
-#' scales::alpha("darkred", 0.4)), |
|
503 |
+#' background = styleColorBar_divergent( |
|
504 |
+#' res_df$log2FoldChange, |
|
505 |
+#' scales::alpha("navyblue", 0.4), |
|
506 |
+#' scales::alpha("darkred", 0.4) |
|
507 |
+#' ), |
|
480 | 508 |
#' backgroundSize = "100% 90%", |
481 | 509 |
#' backgroundRepeat = "no-repeat", |
482 | 510 |
#' backgroundPosition = "center" |
... | ... |
@@ -484,17 +512,19 @@ overlap_jaccard_index <- function(x, y) { |
484 | 512 |
#' |
485 | 513 |
#' |
486 | 514 |
#' simplest_df <- data.frame( |
487 |
-#' a = c(rep("a",9)), |
|
515 |
+#' a = c(rep("a", 9)), |
|
488 | 516 |
#' value = c(-4, -3, -2, -1, 0, 1, 2, 3, 4) |
489 | 517 |
#' ) |
490 | 518 |
#' |
491 | 519 |
#' # or with a very simple data frame |
492 | 520 |
#' DT::datatable(simplest_df) %>% |
493 | 521 |
#' formatStyle( |
494 |
-#' 'value', |
|
495 |
-#' background = styleColorBar_divergent(simplest_df$value, |
|
496 |
-#' scales::alpha("forestgreen", 0.4), |
|
497 |
-#' scales::alpha("gold", 0.4)), |
|
522 |
+#' "value", |
|
523 |
+#' background = styleColorBar_divergent( |
|
524 |
+#' simplest_df$value, |
|
525 |
+#' scales::alpha("forestgreen", 0.4), |
|
526 |
+#' scales::alpha("gold", 0.4) |
|
527 |
+#' ), |
|
498 | 528 |
#' backgroundSize = "100% 90%", |
499 | 529 |
#' backgroundRepeat = "no-repeat", |
500 | 530 |
#' backgroundPosition = "center" |
... | ... |
@@ -502,12 +532,13 @@ overlap_jaccard_index <- function(x, y) { |
502 | 532 |
styleColorBar_divergent <- function(data, |
503 | 533 |
color_pos, |
504 | 534 |
color_neg) { |
505 |
- |
|
506 | 535 |
max_val <- max(abs(data)) |
507 | 536 |
JS( |
508 | 537 |
sprintf( |
509 | 538 |
"isNaN(parseFloat(value)) || value < 0 ? 'linear-gradient(90deg, transparent, transparent ' + (50 + value/%s * 50) + '%%, %s ' + (50 + value/%s * 50) + '%%,%s 50%%,transparent 50%%)': 'linear-gradient(90deg, transparent, transparent 50%%, %s 50%%, %s ' + (50 + value/%s * 50) + '%%, transparent ' + (50 + value/%s * 50) + '%%)'", |
510 |
- max_val, color_pos, max_val, color_pos, color_neg, color_neg, max_val, max_val)) |
|
539 |
+ max_val, color_pos, max_val, color_pos, color_neg, color_neg, max_val, max_val |
|
540 |
+ ) |
|
541 |
+ ) |
|
511 | 542 |
} |
512 | 543 |
|
513 | 544 |
|
... | ... |
@@ -530,21 +561,25 @@ styleColorBar_divergent <- function(data, |
530 | 561 |
#' |
531 | 562 |
#' @examples |
532 | 563 |
#' a <- 1:9 |
533 |
-#' pal <- RColorBrewer::brewer.pal(9,"Set1") |
|
564 |
+#' pal <- RColorBrewer::brewer.pal(9, "Set1") |
|
534 | 565 |
#' map2color(a, pal) |
535 | 566 |
#' plot(a, col = map2color(a, pal), pch = 20, cex = 4) |
536 | 567 |
#' |
537 | 568 |
#' b <- 1:50 |
538 | 569 |
#' pal2 <- grDevices::colorRampPalette( |
539 |
-#' RColorBrewer::brewer.pal(name = "RdYlBu", 11))(50) |
|
570 |
+#' RColorBrewer::brewer.pal(name = "RdYlBu", 11) |
|
571 |
+#' )(50) |
|
540 | 572 |
#' plot(b, col = map2color(b, pal2), pch = 20, cex = 3) |
541 | 573 |
map2color <- function(x, pal, limits = NULL) { |
542 |
- if (is.null(limits)) |
|
574 |
+ if (is.null(limits)) { |
|
543 | 575 |
limits <- range(x) |
576 |
+ } |
|
544 | 577 |
pal[findInterval(x, seq(limits[1], |
545 |
- limits[2], |
|
546 |
- length.out = length(pal) + 1), |
|
547 |
- all.inside = TRUE)] |
|
578 |
+ limits[2], |
|
579 |
+ length.out = length(pal) + 1 |
|
580 |
+ ), |
|
581 |
+ all.inside = TRUE |
|
582 |
+ )] |
|
548 | 583 |
} |
549 | 584 |
|
550 | 585 |
|
... | ... |
@@ -566,14 +601,17 @@ map2color <- function(x, pal, limits = NULL) { |
566 | 601 |
#' check_colors(mypal) |
567 | 602 |
#' mypal2 <- rev( |
568 | 603 |
#' scales::alpha( |
569 |
-#' colorRampPalette(RColorBrewer::brewer.pal(name = "RdYlBu", 11))(50), 0.4)) |
|
604 |
+#' colorRampPalette(RColorBrewer::brewer.pal(name = "RdYlBu", 11))(50), 0.4 |
|
605 |
+#' ) |
|
606 |
+#' ) |
|
570 | 607 |
#' check_colors(mypal2) |
571 | 608 |
#' # useful with long vectors to check at once if all cols are fine |
572 | 609 |
#' all(check_colors(mypal2)) |
573 | 610 |
check_colors <- function(x) { |
574 | 611 |
vapply(x, function(col) { |
575 | 612 |
tryCatch(is.matrix(col2rgb(col)), |
576 |
- error = function(e) FALSE) |
|
613 |
+ error = function(e) FALSE |
|
614 |
+ ) |
|
577 | 615 |
}, logical(1)) |
578 | 616 |
} |
579 | 617 |
|
... | ... |
@@ -598,15 +636,17 @@ check_colors <- function(x) { |
598 | 636 |
#' res_df <- deseqresult2df(res_macrophage_IFNg_vs_naive) |
599 | 637 |
#' head(res_df) |
600 | 638 |
deseqresult2df <- function(res_de, FDR = NULL) { |
601 |
- if (!is(res_de, "DESeqResults")) |
|
639 |
+ if (!is(res_de, "DESeqResults")) { |
|
602 | 640 |
stop("Not a DESeqResults object.") |
641 |
+ } |
|
603 | 642 |
res <- as.data.frame(res_de) |
604 | 643 |
res <- cbind(rownames(res), res) |
605 | 644 |
names(res)[1] <- "id" |
606 | 645 |
res$id <- as.character(res$id) |
607 | 646 |
res <- res[order(res$padj), ] |
608 |
- if (!is.null(FDR)) |
|
647 |
+ if (!is.null(FDR)) { |
|
609 | 648 |
res <- res[!(is.na(res$padj)) & res$padj <= FDR, ] |
649 |
+ } |
|
610 | 650 |
res |
611 | 651 |
} |
612 | 652 |
|
... | ... |
@@ -627,10 +667,9 @@ deseqresult2df <- function(res_de, FDR = NULL) { |
627 | 667 |
#' @examples |
628 | 668 |
#' library("igraph") |
629 | 669 |
#' g <- make_full_graph(5) %du% make_full_graph(5) %du% make_full_graph(5) |
630 |
-#' g <- add_edges(g, c(1,6, 1,11, 6, 11)) |
|
670 |
+#' g <- add_edges(g, c(1, 6, 1, 11, 6, 11)) |
|
631 | 671 |
#' export_to_sif(g, tempfile()) |
632 | 672 |
export_to_sif <- function(g, sif_file = "", edge_label = "relates_to") { |
633 |
- |
|
634 | 673 |
stopifnot(is(g, "igraph")) |
635 | 674 |
stopifnot(is.character(sif_file) & length(sif_file) == 1) |
636 | 675 |
sif_file <- normalizePath(sif_file, mustWork = FALSE) |
... | ... |
@@ -643,8 +682,10 @@ export_to_sif <- function(g, sif_file = "", edge_label = "relates_to") { |
643 | 682 |
n2 = el[, 2] |
644 | 683 |
) |
645 | 684 |
message("Saving the file to ", sif_file) |
646 |
- write.table(sif_df, file = sif_file, sep = "\t", quote = FALSE, |
|
647 |
- col.names = FALSE, row.names = FALSE) |
|
685 |
+ write.table(sif_df, |
|
686 |
+ file = sif_file, sep = "\t", quote = FALSE, |
|
687 |
+ col.names = FALSE, row.names = FALSE |
|
688 |
+ ) |
|
648 | 689 |
message("Done!") |
649 | 690 |
return(invisible(sif_file)) |
650 | 691 |
} |
... | ... |
@@ -677,9 +718,9 @@ GeneTonic_footer <- fluidRow( |
677 | 718 |
|
678 | 719 |
.onLoad <- function(libname, pkgname) { |
679 | 720 |
# Create link to logo |
680 |
- #nocov start |
|
721 |
+ # nocov start |
|
681 | 722 |
shiny::addResourcePath("GeneTonic", system.file("www", package = "GeneTonic")) |
682 |
- #nocov end |
|
723 |
+ # nocov end |
|
683 | 724 |
} |
684 | 725 |
|
685 | 726 |
|
... | ... |
@@ -694,13 +735,15 @@ gt_downloadButton <- function(outputId, |
694 | 735 |
icon = "magic", |
695 | 736 |
class = NULL, |
696 | 737 |
...) { |
697 |
- aTag <- tags$a(id = outputId, |
|
698 |
- class = paste("btn btn-default shiny-download-link", class), |
|
699 |
- href = "", |
|
700 |
- target = "_blank", |
|
701 |
- download = NA, |
|
702 |
- icon(icon), |
|
703 |
- label) |
|
738 |
+ aTag <- tags$a( |
|
739 |
+ id = outputId, |
|
740 |
+ class = paste("btn btn-default shiny-download-link", class), |
|
741 |
+ href = "", |
|
742 |
+ target = "_blank", |
|
743 |
+ download = NA, |
|
744 |
+ icon(icon), |
|
745 |
+ label |
|
746 |
+ ) |
|
704 | 747 |
} |
705 | 748 |
|
706 | 749 |
|
... | ... |
@@ -2,16 +2,16 @@ |
2 | 2 |
#' |
3 | 3 |
#' `GeneTonic` is a Bioconductor package that provides an interactive Shiny-based |
4 | 4 |
#' graphical user interface for streamlining the interpretation of RNA-seq data |
5 |
-#' |
|
6 |
-#' `GeneTonic` simplifies and optimizes the integration of all components of |
|
7 |
-#' Diffeential Expression analysis, with functional enrichment analyis and the |
|
5 |
+#' |
|
6 |
+#' `GeneTonic` simplifies and optimizes the integration of all components of |
|
7 |
+#' Diffeential Expression analysis, with functional enrichment analyis and the |
|
8 | 8 |
#' original expression quantifications. |
9 |
-#' It does so in a way that makes it easier to generate insightful observations |
|
10 |
-#' and hypothesis - combining the benefits of interactivity and reproducibility, |
|
11 |
-#' e.g. by capturing the features and gene sets of interest highlighted during |
|
12 |
-#' the live session, and creating an HTML report as an artifact where text, |
|
9 |
+#' It does so in a way that makes it easier to generate insightful observations |
|
10 |
+#' and hypothesis - combining the benefits of interactivity and reproducibility, |
|
11 |
+#' e.g. by capturing the features and gene sets of interest highlighted during |
|
12 |
+#' the live session, and creating an HTML report as an artifact where text, |
|
13 | 13 |
#' code, and output coexist. |
14 |
-#' |
|
14 |
+#' |
|
15 | 15 |
#' @author Federico Marini \email{marinif@@uni-mainz.de} |
16 | 16 |
#' |
17 | 17 |
#' @importFrom AnnotationDbi Definition GOID Ontology Secondary Synonym Term |
... | ... |
@@ -61,7 +61,7 @@ |
61 | 61 |
#' @importFrom tidyr separate_rows pivot_longer |
62 | 62 |
#' @importFrom tools file_ext file_path_sans_ext |
63 | 63 |
#' @importFrom utils read.delim sessionInfo browseURL citation data write.table |
64 |
-#' @importFrom visNetwork renderVisNetwork visExport visIgraph visNetworkOutput |
|
64 |
+#' @importFrom visNetwork renderVisNetwork visExport visIgraph visNetworkOutput |
|
65 | 65 |
#' visOptions |
66 | 66 |
#' @importFrom viridis viridis |
67 | 67 |
#' |
... | ... |
@@ -43,7 +43,7 @@ |
43 | 43 |
#' |
44 | 44 |
#' # dds object |
45 | 45 |
#' data("gse", package = "macrophage") |
46 |
-#' dds_macrophage <- DESeqDataSet(gse, design = ~line + condition) |
|
46 |
+#' dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition) |
|
47 | 47 |
#' rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15) |
48 | 48 |
#' dds_macrophage <- estimateSizeFactors(dds_macrophage) |
49 | 49 |
#' |
... | ... |
@@ -51,9 +51,10 @@ |
51 | 51 |
#' anno_df <- data.frame( |
52 | 52 |
#' gene_id = rownames(dds_macrophage), |
53 | 53 |
#' gene_name = mapIds(org.Hs.eg.db, |
54 |
-#' keys = rownames(dds_macrophage), |
|
55 |
-#' column = "SYMBOL", |
|
56 |
-#' keytype = "ENSEMBL"), |
|
54 |
+#' keys = rownames(dds_macrophage), |
|
55 |
+#' column = "SYMBOL", |
|
56 |
+#' keytype = "ENSEMBL" |
|
57 |
+#' ), |
|
57 | 58 |
#' stringsAsFactors = FALSE, |
58 | 59 |
#' row.names = rownames(dds_macrophage) |
59 | 60 |
#' ) |
... | ... |
@@ -69,17 +70,22 @@ |
69 | 70 |
#' res_enrich <- get_aggrscores(res_enrich, res_de, anno_df) |
70 | 71 |
#' |
71 | 72 |
#' # now everything is in place to launch the app |
72 |
-#' if (interactive()) |
|
73 |
-#' GeneTonic(dds = dds_macrophage, |
|
74 |
-#' res_de = res_de, |
|
75 |
-#' res_enrich = res_enrich, |
|
76 |
-#' annotation_obj = anno_df, |
|
77 |
-#' project_id = "myexample") |
|
73 |
+#' if (interactive()) { |
|
74 |
+#' GeneTonic( |
|
75 |
+#' dds = dds_macrophage, |
|
76 |
+#' res_de = res_de, |
|
77 |
+#' res_enrich = res_enrich, |
|
78 |
+#' annotation_obj = anno_df, |
|
79 |
+#' project_id = "myexample" |
|
80 |
+#' ) |
|
81 |
+#' } |
|
78 | 82 |
#' # alternatively... |
79 |
-#' gtl_macrophage <- GeneTonic_list(dds = dds_macrophage, |
|
80 |
-#' res_de = res_de, |
|
81 |
-#' res_enrich = res_enrich, |
|
82 |
-#' annotation_obj = anno_df) |
|
83 |
+#' gtl_macrophage <- GeneTonic_list( |
|
84 |
+#' dds = dds_macrophage, |
|
85 |
+#' res_de = res_de, |
|
86 |
+#' res_enrich = res_enrich, |
|
87 |
+#' annotation_obj = anno_df |
|
88 |
+#' ) |
|
83 | 89 |
#' # GeneTonic(gtl = gtl_macrophage) |
84 | 90 |
GeneTonic <- function(dds, |
85 | 91 |
res_de, |
... | ... |
@@ -105,15 +111,19 @@ GeneTonic <- function(dds, |
105 | 111 |
} |
106 | 112 |
|
107 | 113 |
# checks on the objects provided |
108 |
- checkup_GeneTonic(dds, |
|
109 |
- res_de, |
|
110 |
- res_enrich, |
|
111 |
- annotation_obj) |
|
114 |
+ checkup_GeneTonic( |
|
115 |
+ dds, |
|
116 |
+ res_de, |
|
117 |
+ res_enrich, |
|
118 |
+ annotation_obj |
|
119 |
+ ) |
|
112 | 120 |
|
113 | 121 |
# clean up the result object, e.g. removing the NAs in the relevant columns |
114 | 122 |
removed_genes <- is.na(res_de$log2FoldChange) |
115 |
- message("Removing ", sum(removed_genes), |
|
116 |
- "/", nrow(res_de), " rows from the DE `res_de` object - log2FC values detected as NA") |
|
123 |
+ message( |
|
124 |
+ "Removing ", sum(removed_genes), |
|
125 |
+ "/", nrow(res_de), " rows from the DE `res_de` object - log2FC values detected as NA" |
|
126 |
+ ) |
|
117 | 127 |
res_de <- res_de[!removed_genes, ] |
118 | 128 |
|
119 | 129 |
# UI definition ----------------------------------------------------------- |
... | ... |
@@ -128,8 +138,10 @@ GeneTonic <- function(dds, |
128 | 138 |
# older leftUi elements |
129 | 139 |
tagList( |
130 | 140 |
tags$code(tags$h3("GeneTonic")), |
131 |
- actionButton("bookmarker", label = "Bookmark", icon = icon("heart"), |
|
132 |
- style = "color: #ffffff; background-color: #ac0000; border-color: #ffffff", class = "ml-5") |
|
141 |
+ actionButton("bookmarker", |
|
142 |
+ label = "Bookmark", icon = icon("heart"), |
|
143 |
+ style = "color: #ffffff; background-color: #ac0000; border-color: #ffffff", class = "ml-5" |
|
144 |
+ ) |
|
133 | 145 |
), |
134 | 146 |
# older rightUi elements |
135 | 147 |
# ideally to be spaced on the full right side... |
... | ... |
@@ -150,8 +162,9 @@ GeneTonic <- function(dds, |
150 | 162 |
icon = icon("book-open"), |
151 | 163 |
label = "Open GeneTonic Vignette", style = .actionbutton_biocstyle, |
152 | 164 |
onclick = ifelse(system.file("doc", "GeneTonic_manual.html", package = "GeneTonic") != "", |
153 |
- "", |
|
154 |
- "window.open('https://federicomarini.github.io/GeneTonic/articles/GeneTonic_manual.html', '_blank')") |
|
165 |
+ "", |
|
166 |
+ "window.open('https://federicomarini.github.io/GeneTonic/articles/GeneTonic_manual.html', '_blank')" |
|
167 |
+ ) |
|
155 | 168 |
# sprintf("window.open('http://bioconductor.org/packages/%s/bioc/vignettes/GeneTonic/inst/doc/GeneTonic_manual.html', '_blank')", |
156 | 169 |
# ifelse(unlist(packageVersion("GeneTonic"))[2] %% 2L==0L, "release", "devel") |
157 | 170 |
# ) |
... | ... |
@@ -187,7 +200,7 @@ GeneTonic <- function(dds, |
187 | 200 |
), |
188 | 201 |
title = bs4Dash::bs4DashBrand( |
189 | 202 |
title = HTML("<small>GeneTonic</small>"), |
190 |
- href = "https://bioconductor.org/packages/GeneTonic", |
|
203 |
+ href = "https://bioconductor.org/packages/GeneTonic", |
|
191 | 204 |
# color = "info", |
192 | 205 |
image = "GeneTonic/GeneTonic.png" |
193 | 206 |
), |
... | ... |
@@ -195,9 +208,9 @@ GeneTonic <- function(dds, |
195 | 208 |
status = "gray-dark", |
196 | 209 |
border = FALSE, |
197 | 210 |
controlbarIcon = icon("gears"), |
198 |
- fixed = TRUE #, |
|
199 |
- # leftUi = |
|
200 |
- # rightUi = |
|
211 |
+ fixed = TRUE # , |
|
212 |
+ # leftUi = |
|
213 |
+ # rightUi = |
|
201 | 214 |
), |
202 | 215 |
|
203 | 216 |
# sidebar definition ------------------------------------------------------ |
... | ... |
@@ -212,7 +225,6 @@ GeneTonic <- function(dds, |
212 | 225 |
# src = "logos/online-learning.png", |
213 | 226 |
elevation = 1, |
214 | 227 |
opacity = 0.8, |
215 |
- |
|
216 | 228 |
bs4SidebarMenu( |
217 | 229 |
id = "gt_tabs", |
218 | 230 |
bs4SidebarMenuItem( |
... | ... |
@@ -272,13 +284,11 @@ GeneTonic <- function(dds, |
272 | 284 |
) |
273 | 285 |
) |
274 | 286 |
), |
275 |
- |
|
276 | 287 |
tags$head( |
277 | 288 |
tags$style( |
278 | 289 |
".biocdlbutton{background-color:#0092AC;} .biocdlbutton{color: #ffffff;}" |
279 | 290 |
) |
280 | 291 |
), |
281 |
- |
|
282 | 292 |
tags$script(HTML("$(function(){ |
283 | 293 |
$(document).keyup(function(e) { |
284 | 294 |
if (e.which == 17) { |
... | ... |
@@ -307,7 +317,8 @@ GeneTonic <- function(dds, |
307 | 317 |
column( |
308 | 318 |
width = 1, |
309 | 319 |
actionButton( |
310 |
- "tour_firststeps", label = "", icon = icon("question-circle"), |
|
320 |
+ "tour_firststeps", |
|
321 |
+ label = "", icon = icon("question-circle"), |
|
311 | 322 |
style = .helpbutton_biocstyle |
312 | 323 |
) |
313 | 324 |
) |
... | ... |
@@ -374,7 +385,8 @@ GeneTonic <- function(dds, |
374 | 385 |
column( |
375 | 386 |
width = 1, |
376 | 387 |
actionButton( |
377 |
- "tour_ggs", label = "", icon = icon("question-circle"), |
|
388 |
+ "tour_ggs", |
|
389 |
+ label = "", icon = icon("question-circle"), |
|
378 | 390 |
style = .helpbutton_biocstyle |
379 | 391 |
) |
380 | 392 |
) |
... | ... |
@@ -384,8 +396,9 @@ GeneTonic <- function(dds, |
384 | 396 |
width = 8, |
385 | 397 |
withSpinner( |
386 | 398 |
visNetworkOutput("ggsnetwork", |
387 |
- height = "700px", |
|
388 |
- width = "100%") |
|
399 |
+ height = "700px", |
|
400 |
+ width = "100%" |
|
401 |
+ ) |
|
389 | 402 |
) |
390 | 403 |
), |
391 | 404 |
column( |
... | ... |
@@ -406,7 +419,6 @@ GeneTonic <- function(dds, |
406 | 419 |
) |
407 | 420 |
) |
408 | 421 |
), |
409 |
- |
|
410 | 422 |
fluidRow( |
411 | 423 |
bs4Dash::bs4Card( |
412 | 424 |
width = 12, |
... | ... |
@@ -421,11 +433,13 @@ GeneTonic <- function(dds, |
421 | 433 |
column( |
422 | 434 |
width = 8, |
423 | 435 |
uiOutput("ui_backbone_launch"), |
424 |
- radioButtons(inputId = "backbone_on", |
|
425 |
- label = "Compute the backbone on", |
|
426 |
- choices = c("genesets", "features"), |
|
427 |
- selected = "genesets", |
|
428 |
- inline = TRUE), |
|
436 |
+ radioButtons( |
|
437 |
+ inputId = "backbone_on", |
|
438 |
+ label = "Compute the backbone on", |
|
439 |
+ choices = c("genesets", "features"), |
|
440 |
+ selected = "genesets", |
|
441 |
+ inline = TRUE |
|
442 |
+ ), |
|
429 | 443 |
withSpinner( |
430 | 444 |
visNetworkOutput("backbone_graph") |
431 | 445 |
) |
... | ... |
@@ -437,7 +451,6 @@ GeneTonic <- function(dds, |
437 | 451 |
) |
438 | 452 |
) |
439 | 453 |
) |
440 |
- |
|
441 | 454 |
), |
442 | 455 |
|
443 | 456 |
# ui panel enrichment map ------------------------------------------------- |
... | ... |
@@ -450,7 +463,8 @@ GeneTonic <- function(dds, |
450 | 463 |
column( |
451 | 464 |
width = 1, |
452 | 465 |
actionButton( |
453 |
- "tour_emap", label = "", icon = icon("question-circle"), |
|
466 |
+ "tour_emap", |
|
467 |
+ label = "", icon = icon("question-circle"), |
|
454 | 468 |
style = .helpbutton_biocstyle |
455 | 469 |
) |
456 | 470 |
) |
... | ... |
@@ -464,10 +478,12 @@ GeneTonic <- function(dds, |
464 | 478 |
inputId = "emap_colorby", |
465 | 479 |
label = "Color emap by", |
466 | 480 |
choices = colnames(res_enrich)[unlist(lapply(res_enrich, is.numeric))], |
467 |
- selected = "gs_pvalue"), |
|
481 |
+ selected = "gs_pvalue" |
|
482 |
+ ), |
|
468 | 483 |
visNetworkOutput("emap_visnet", |
469 |
- height = "700px", |
|
470 |
- width = "100%") |
|
484 |
+ height = "700px", |
|
485 |
+ width = "100%" |
|
486 |
+ ) |
|
471 | 487 |
) |
472 | 488 |
) |
473 | 489 |
), |
... | ... |
@@ -497,7 +513,6 @@ GeneTonic <- function(dds, |
497 | 513 |
withSpinner( |
498 | 514 |
DT::dataTableOutput("dt_distill") |
499 | 515 |
), |
500 |
- |
|
501 | 516 |
uiOutput("distill_launch"), |
502 | 517 |
numericInput( |
503 | 518 |
inputId = "n_genesets_distill", |
... | ... |
@@ -529,12 +544,12 @@ GeneTonic <- function(dds, |
529 | 544 |
column( |
530 | 545 |
width = 1, |
531 | 546 |
actionButton( |
532 |
- "tour_overview", label = "", icon = icon("question-circle"), |
|
547 |
+ "tour_overview", |
|
548 |
+ label = "", icon = icon("question-circle"), |
|
533 | 549 |
style = .helpbutton_biocstyle |
534 | 550 |
) |
535 | 551 |
) |
536 | 552 |
), |
537 |
- |
|
538 | 553 |
fluidRow( |
539 | 554 |
bs4Dash::column( |
540 | 555 |
width = 11, |
... | ... |
@@ -555,25 +570,31 @@ GeneTonic <- function(dds, |
555 | 570 |
tabPanel( |
556 | 571 |
title = "Geneset Volcano", |
557 | 572 |
withSpinner(plotOutput("gs_volcano", |
558 |
- height = "650px")) |
|
573 |
+ height = "650px" |
|
574 |
+ )) |
|
559 | 575 |
), |
560 | 576 |
shiny::tabPanel( |
561 | 577 |
title = "Geneset Volcano - simplified", |
562 |
- numericInput(inputId = "gs_overlap", |
|
563 |
- label = "Gene Set overlap", |
|
564 |
- value = 0.6, min = 0, max = 1, step = 0.05), |
|
578 |
+ numericInput( |
|
579 |
+ inputId = "gs_overlap", |
|
580 |
+ label = "Gene Set overlap", |
|
581 |
+ value = 0.6, min = 0, max = 1, step = 0.05 |
|
582 |
+ ), |
|
565 | 583 |
withSpinner(plotOutput("gs_volcano_simplified", |
566 |
- height = "650px")) |
|
584 |
+ height = "650px" |
|
585 |
+ )) |
|
567 | 586 |
), |
568 | 587 |
shiny::tabPanel( |
569 | 588 |
title = "Enhanced Table", |
570 | 589 |
withSpinner(plotOutput("enriched_funcres", |
571 |
- height = "650px")) |
|
590 |
+ height = "650px" |
|
591 |
+ )) |
|
572 | 592 |
), |
573 | 593 |
shiny::tabPanel( |
574 | 594 |
title = "Enhanced Table - interactive", |
575 | 595 |
withSpinner(plotlyOutput("enriched_funcres_plotly", |
576 |
- height = "650px")) |
|
596 |
+ height = "650px" |
|
597 |
+ )) |
|
577 | 598 |
) |
578 | 599 |
) |
579 | 600 |
) |
... | ... |
@@ -591,12 +612,12 @@ GeneTonic <- function(dds, |
591 | 612 |
column( |
592 | 613 |
width = 1, |
593 | 614 |
actionButton( |
594 |
- "tour_gsviz", label = "", icon = icon("question-circle"), |
|
615 |
+ "tour_gsviz", |
|
616 |
+ label = "", icon = icon("question-circle"), |
|
595 | 617 |
style = .helpbutton_biocstyle |
596 | 618 |
) |
597 | 619 |
) |
598 | 620 |
), |
599 |
- |
|
600 | 621 |
fluidRow( |
601 | 622 |
bs4Dash::column( |
602 | 623 |
width = 11, |
... | ... |
@@ -616,38 +637,44 @@ GeneTonic <- function(dds, |
616 | 637 |
shiny::tabPanel( |
617 | 638 |
title = "Scores Heatmap", |
618 | 639 |
withSpinner(plotOutput("gsscores_heatmap", |
619 |
- height = "650px")) |
|
620 |
- |
|
640 |
+ height = "650px" |
|
641 |
+ )) |
|
621 | 642 |
), |
622 | 643 |
shiny::tabPanel( |
623 | 644 |
title = "Alluvial Plot", |
624 | 645 |
withSpinner(plotlyOutput("alluvial_genesets", |
625 |
- height = "650px")) |
|
646 |
+ height = "650px" |
|
647 |
+ )) |
|
626 | 648 |
), |
627 | 649 |
shiny::tabPanel( |
628 | 650 |
title = "Summary Heatmap", |
629 | 651 |
withSpinner(plotOutput("gs_summaryheat", |
630 |
- height = "650px")) |
|
652 |
+ height = "650px" |
|
653 |
+ )) |
|
631 | 654 |
), |
632 | 655 |
shiny::tabPanel( |
633 | 656 |
title = "Geneset MDS", |
634 | 657 |
withSpinner(plotOutput("mds_genesets", |
635 |
- height = "650px")) |
|
658 |
+ height = "650px" |
|
659 |
+ )) |
|
636 | 660 |
), |
637 | 661 |
shiny::tabPanel( |
638 | 662 |
title = "Summary Overview", |
639 | 663 |
withSpinner(plotOutput("gs_summaryoverview", |
640 |
- height = "650px")) |
|
664 |
+ height = "650px" |
|
665 |
+ )) |
|
641 | 666 |
), |
642 | 667 |
shiny::tabPanel( |
643 | 668 |
title = "Geneset Radar", |
644 | 669 |
withSpinner(plotlyOutput("gs_summaryradar", |
645 |
- height = "650px")) |
|
670 |
+ height = "650px" |
|
671 |
+ )) |
|
646 | 672 |
), |
647 | 673 |
shiny::tabPanel( |
648 | 674 |
title = "Geneset Dendrogram", |
649 | 675 |
withSpinner(plotOutput("gs_dendro", |
650 |
- height = "650px")) |
|
676 |
+ height = "650px" |
|
677 |
+ )) |
|
651 | 678 |
) |
652 | 679 |
) |
653 | 680 |
) |
... | ... |
@@ -665,7 +692,8 @@ GeneTonic <- function(dds, |
665 | 692 |
column( |
666 | 693 |
width = 1, |
667 | 694 |
actionButton( |
668 |
- "tour_bookmarks", label = "", icon = icon("question-circle"), |
|
695 |
+ "tour_bookmarks", |
|
696 |
+ label = "", icon = icon("question-circle"), |
|
669 | 697 |
style = .helpbutton_biocstyle |
670 | 698 |
) |
671 | 699 |
) |
... | ... |
@@ -685,7 +713,8 @@ GeneTonic <- function(dds, |
685 | 713 |
"start_happyhour", |
686 | 714 |
"Start the happy hour!", |
687 | 715 |
class = "biocdlbutton", |
688 |
- icon = "cocktail") # magic? |
|
716 |
+ icon = "cocktail" |
|
717 |
+ ) # magic? |
|
689 | 718 |
) |
690 | 719 |
), |
691 | 720 |
hr(), |
... | ... |
@@ -694,7 +723,8 @@ GeneTonic <- function(dds, |
694 | 723 |
column( |
695 | 724 |
width = 4, |
696 | 725 |
textInput( |
697 |
- "se_export_name",label = "Choose a filename for the serialized .rds object", |
|
726 |
+ "se_export_name", |
|
727 |
+ label = "Choose a filename for the serialized .rds object", |
|
698 | 728 |
value = "se_GeneTonic_toiSEE.rds" |
699 | 729 |
) |
700 | 730 |
), |
... | ... |
@@ -714,17 +744,24 @@ GeneTonic <- function(dds, |
714 | 744 |
# controlbar definition --------------------------------------------------- |
715 | 745 |
controlbar = bs4Dash::bs4DashControlbar( |
716 | 746 |
collapsed = TRUE, |
717 |
- numericInput(inputId = "de_fdr", |
|
718 |
- label = "False Discovery Rate (FDR) for DE", |
|
719 |
- value = 0.05, min = 0.0001, max = 1, step = 0.01), |
|
720 |
- numericInput(inputId = "n_genesets", |
|
721 |
- label = "Number of genesets", |
|
722 |
- value = 15, min = 1, max = nrow(res_enrich)), |
|
723 |
- selectInput("exp_condition", label = "Group/color by: ", |
|
724 |
- choices = c(NULL, names(colData(dds))), selected = NULL, multiple = TRUE), |
|
747 |
+ numericInput( |
|
748 |
+ inputId = "de_fdr", |
|
749 |
+ label = "False Discovery Rate (FDR) for DE", |
|
750 |
+ value = 0.05, min = 0.0001, max = 1, step = 0.01 |
|
751 |
+ ), |
|
752 |
+ numericInput( |
|
753 |
+ inputId = "n_genesets", |
|
754 |
+ label = "Number of genesets", |
|
755 |
+ value = 15, min = 1, max = nrow(res_enrich) |
|
756 |
+ ), |
|
757 |
+ selectInput("exp_condition", |
|
758 |
+ label = "Group/color by: ", |
|
759 |
+ choices = c(NULL, names(colData(dds))), selected = NULL, multiple = TRUE |
|
760 |
+ ), |
|
725 | 761 |
colourInput("col", "Select colour for volcano plot", "#1a81c2", |
726 |
- returnName = TRUE, |
|
727 |
- allowTransparent = TRUE), |
|
762 |
+ returnName = TRUE, |
|
763 |
+ allowTransparent = TRUE |
|
764 |
+ ), |
|
728 | 765 |
checkboxInput("labels", label = "Display all labels", value = FALSE) |
729 | 766 |
), |
730 | 767 |
|
... | ... |
@@ -733,12 +770,11 @@ GeneTonic <- function(dds, |
733 | 770 |
left = GeneTonic_footer, |
734 | 771 |
right = NULL |
735 | 772 |
) |
736 |
- |
|
737 | 773 |
) |
738 | 774 |
|
739 | 775 |
options(shiny.maxRequestSize = 15 * 1024^2) |
740 | 776 |
|
741 |
- #nocov start |
|
777 |
+ # nocov start |
|
742 | 778 |
genetonic_server <- function(input, output, session) { |
743 | 779 |
|
744 | 780 |
# reactive objects and setup commands ------------------------------------- |
... | ... |
@@ -749,9 +785,11 @@ GeneTonic <- function(dds, |
749 | 785 |
|
750 | 786 |
myvst <- vst(dds) |
751 | 787 |
|
752 |
- res_enhanced <- get_aggrscores(res_enrich = res_enrich, |
|
753 |
- res_de = res_de, |
|
754 |
- annotation_obj = annotation_obj) |
|
788 |
+ res_enhanced <- get_aggrscores( |
|
789 |
+ res_enrich = res_enrich, |
|
790 |
+ res_de = res_de, |
|
791 |
+ annotation_obj = annotation_obj |
|
792 |
+ ) |
|
755 | 793 |
|
756 | 794 |
# output$ui_exp_condition <- renderUI({ |
757 | 795 |
# selectInput("exp_condition", label = "Group/color by: ", |
... | ... |
@@ -783,9 +821,11 @@ GeneTonic <- function(dds, |
783 | 821 |
formatRound(columns = c("log2FoldChange"), digits = 3) %>% |
784 | 822 |
formatStyle( |
785 | 823 |
"log2FoldChange", |
786 |
- background = styleColorBar_divergent(as.data.frame(res_de)$log2FoldChange, |
|
787 |
- scales::alpha("navyblue", 0.4), |
|
788 |
- scales::alpha("darkred", 0.4)), |
|
824 |
+ background = styleColorBar_divergent( |
|
825 |
+ as.data.frame(res_de)$log2FoldChange, |
|
826 |
+ scales::alpha("navyblue", 0.4), |
|
827 |
+ scales::alpha("darkred", 0.4) |
|
828 |
+ ), |
|
789 | 829 |
backgroundSize = "100% 90%", |
790 | 830 |
backgroundRepeat = "no-repeat", |
791 | 831 |
backgroundPosition = "center" |
... | ... |
@@ -891,14 +931,19 @@ GeneTonic <- function(dds, |
891 | 931 |
# minimal example |
892 | 932 |
|
893 | 933 |
visNetwork::visIgraph(reactive_values$ggs_graph()) %>% |
894 |
- visOptions(highlightNearest = list(enabled = TRUE, |
|
895 |
- degree = 1, |
|
896 |
- hover = TRUE), |
|
897 |
- nodesIdSelection = TRUE) %>% |
|
898 |
- visExport(name = "ggs_network", |
|
899 |
- type = "png", |
|
900 |
- label = "Save ggs graph") |
|
901 |
- |
|
934 |
+ visOptions( |
|
935 |
+ highlightNearest = list( |
|
936 |
+ enabled = TRUE, |
|
937 |
+ degree = 1, |
|
938 |
+ hover = TRUE |
|
939 |
+ ), |
|
940 |
+ nodesIdSelection = TRUE |
|
941 |
+ ) %>% |
|
942 |
+ visExport( |
|
943 |
+ name = "ggs_network", |
|
944 |
+ type = "png", |
|
945 |
+ label = "Save ggs graph" |
|
946 |
+ ) |
|
902 | 947 |
}) |
903 | 948 |
|
904 | 949 |
output$netnode <- renderPrint({ |
... | ... |
@@ -918,7 +963,6 @@ GeneTonic <- function(dds, |
918 | 963 |
h4("Highly connected genes"), |
919 | 964 |
DT::dataTableOutput("table_graph_summary") |
920 | 965 |
) |
921 |
- |
|
922 | 966 |
}) |
923 | 967 |
|
924 | 968 |
output$table_graph_summary <- DT::renderDataTable({ |
... | ... |
@@ -926,7 +970,6 @@ GeneTonic <- function(dds, |
926 | 970 |
|
927 | 971 |
node_degrees <- summarize_ggs_hubgenes(g) |
928 | 972 |
DT::datatable(node_degrees, escape = FALSE) |
929 |
- |
|
930 | 973 |
}) |
931 | 974 |
|
932 | 975 |
output$ui_ggs_genesetbox <- renderUI({ |
... | ... |
@@ -944,7 +987,7 @@ GeneTonic <- function(dds, |
944 | 987 |
cur_node <- match(cur_sel, V(g)$name) |
945 | 988 |
cur_nodetype <- V(g)$nodetype[cur_node] |
946 | 989 |
validate(need(cur_nodetype == "GeneSet", |
947 |
- message = "Please select a gene set from the Gene-Geneset Graph." |
|
990 |
+ message = "Please select a gene set from the Gene-Geneset Graph." |
|
948 | 991 |
)) |
949 | 992 |
cur_gsid <- res_enrich$gs_id[match(input$ggsnetwork_selected, res_enrich$gs_description)] |
950 | 993 |
|
... | ... |
@@ -986,7 +1029,7 @@ GeneTonic <- function(dds, |
986 | 1029 |
cur_node <- match(cur_sel, V(g)$name) |
987 | 1030 |
cur_nodetype <- V(g)$nodetype[cur_node] |
988 | 1031 |
validate(need(cur_nodetype == "GeneSet", |
989 |
- message = "" |
|
1032 |
+ message = "" |
|
990 | 1033 |
)) |
991 | 1034 |
cur_gsid <- res_enrich$gs_id[match(input$ggsnetwork_selected, res_enrich$gs_description)] |
992 | 1035 |
|
... | ... |
@@ -1008,7 +1051,7 @@ GeneTonic <- function(dds, |
1008 | 1051 |
geneset_id = cur_gsid, |
1009 | 1052 |
FDR = input$de_fdr, |
1010 | 1053 |
color = input$col |
1011 |
- ) |
|
1054 |
+ ) |
|
1012 | 1055 |
} |
1013 | 1056 |
}) |
1014 | 1057 |
|
... | ... |
@@ -1018,7 +1061,7 @@ GeneTonic <- function(dds, |
1018 | 1061 |
cur_node <- match(cur_sel, V(g)$name) |
1019 | 1062 |
cur_nodetype <- V(g)$nodetype[cur_node] |
1020 | 1063 |
validate(need(cur_nodetype == "GeneSet", |
1021 |
- message = "" # "Please select a gene set." |
|
1064 |
+ message = "" # "Please select a gene set." |
|
1022 | 1065 |
)) |
1023 | 1066 |
cur_gsid <- res_enrich$gs_id[match(input$ggsnetwork_selected, res_enrich$gs_description)] |
1024 | 1067 |
|
... | ... |
@@ -1038,7 +1081,7 @@ GeneTonic <- function(dds, |
1038 | 1081 |
cur_node <- match(cur_sel, V(g)$name) |
1039 | 1082 |
cur_nodetype <- V(g)$nodetype[cur_node] |
1040 | 1083 |
validate(need(cur_nodetype == "Feature", |
1041 |
- message = "Please select a gene/feature." |
|
1084 |
+ message = "Please select a gene/feature." |
|
1042 | 1085 |
)) |
1043 | 1086 |
|
1044 | 1087 |
cur_geneid <- annotation_obj$gene_id[match(cur_sel, annotation_obj$gene_name)] |
... | ... |
@@ -1056,22 +1099,21 @@ GeneTonic <- function(dds, |
1056 | 1099 |
cur_node <- match(cur_sel, V(g)$name) |
1057 | 1100 |
cur_nodetype <- V(g)$nodetype[cur_node] |
1058 | 1101 |
validate(need(cur_nodetype == "Feature", |
1059 |
- message = "" # "Please select a gene/feature." |
|
1102 |
+ message = "" # "Please select a gene/feature." |
|
1060 | 1103 |
)) |
1061 | 1104 |
validate(need(input$exp_condition != "", |
1062 |
- message = "Please select a group for the experimental condition." |
|
1105 |
+ message = "Please select a group for the experimental condition." |
|
1063 | 1106 |
)) |
1064 | 1107 |
|
1065 | 1108 |
cur_geneid <- annotation_obj$gene_id[match(cur_sel, annotation_obj$gene_name)] |
1066 | 1109 |
gene_plot(dds, |
1067 |
- gene = cur_geneid, |
|
1068 |
- intgroup = input$exp_condition, |
|
1069 |
- annotation_obj = annotation_obj |
|
1110 |
+ gene = cur_geneid, |
|
1111 |
+ intgroup = input$exp_condition, |
|
1112 |
+ annotation_obj = annotation_obj |
|
1070 | 1113 |
) |
1071 | 1114 |
}) |
1072 | 1115 |
|
1073 | 1116 |
reactive_values$backbone_graph <- reactive({ |
1074 |
- |
|
1075 | 1117 |
not_msg <- sprintf("Computing backbone on %s of the current gene-geneset graph, please hold on...", input$backbone_on) |
1076 | 1118 |
showNotification(not_msg) |
1077 | 1119 |
|
... | ... |
@@ -1091,18 +1133,28 @@ GeneTonic <- function(dds, |
1091 | 1133 |
# minimal example |
1092 | 1134 |
bbg <- reactive_values$backbone_graph() |
1093 | 1135 |
validate( |
1094 |
- need({igraph::vcount(bbg) > 0}, message = "Graph has no nodes, try increasing the number of sets to include...") |
|
1136 |
+ need( |
|
1137 |
+ { |
|
1138 |
+ igraph::vcount(bbg) > 0 |
|
1139 |
+ }, |
|
1140 |
+ message = "Graph has no nodes, try increasing the number of sets to include..." |
|
1141 |
+ ) |
|
1095 | 1142 |
) |
1096 | 1143 |
|
1097 | 1144 |
visNetwork::visIgraph(bbg) %>% |
1098 |
- visOptions(highlightNearest = list(enabled = TRUE, |
|
1099 |
- degree = 1, |
|
1100 |
- hover = TRUE), |
|
1101 |
- nodesIdSelection = TRUE) %>% |
|
1102 |
- visExport(name = "backbone_network", |
|
1103 |
- type = "png", |
|
1104 |
- label = "Save backbone graph") |
|
1105 |
- |
|
1145 |
+ visOptions( |
|
1146 |
+ highlightNearest = list( |
|
1147 |
+ enabled = TRUE, |
|
1148 |
+ degree = 1, |
|
1149 |
+ hover = TRUE |
|
1150 |
+ ), |
|
1151 |
+ nodesIdSelection = TRUE |
|
1152 |
+ ) %>% |
|
1153 |
+ visExport( |
|
1154 |
+ name = "backbone_network", |
|
1155 |
+ type = "png", |
|
1156 |
+ label = "Save backbone graph" |
|
1157 |
+ ) |
|
1106 | 1158 |
}) |
1107 | 1159 |
|
1108 | 1160 |
|
... | ... |
@@ -1123,16 +1175,20 @@ GeneTonic <- function(dds, |
1123 | 1175 |
}) |
1124 | 1176 |
|
1125 | 1177 |
output$emap_visnet <- renderVisNetwork({ |
1126 |
- |
|
1127 | 1178 |
visNetwork::visIgraph(emap_graph()) %>% |
1128 |
- visOptions(highlightNearest = list(enabled = TRUE, |
|
1129 |
- degree = 1, |
|
1130 |
- hover = TRUE), |
|
1131 |
- nodesIdSelection = TRUE) %>% |
|
1132 |
- visExport(name = "emap_network", |
|
1133 |
- type = "png", |
|
1134 |
- label = "Save enrichment map") |
|
1135 |
- |
|
1179 |
+ visOptions( |
|
1180 |
+ highlightNearest = list( |
|
1181 |
+ enabled = TRUE, |
|
1182 |
+ degree = 1, |
|
1183 |
+ hover = TRUE |
|
1184 |
+ ), |
|
1185 |
+ nodesIdSelection = TRUE |
|
1186 |
+ ) %>% |
|
1187 |
+ visExport( |
|
1188 |
+ name = "emap_network", |
|
1189 |
+ type = "png", |
|
1190 |
+ label = "Save enrichment map" |
|
1191 |
+ ) |
|
1136 | 1192 |
}) |
1137 | 1193 |
|
1138 | 1194 |
output$ui_emap_sidecontent <- renderUI({ |
... | ... |
@@ -1145,7 +1201,8 @@ GeneTonic <- function(dds, |
1145 | 1201 |
output$emap_geneset_info <- renderUI({ |
1146 | 1202 |
cur_gsid <- res_enrich$gs_id[match(input$emap_visnet_selected, res_enrich$gs_description)] |
1147 | 1203 |
validate(need(!is.na(cur_gsid), |
1148 |
- message = "")) |
|
1204 |
+ message = "" |
|
1205 |
+ )) |
|
1149 | 1206 |
|
1150 | 1207 |
# message(cur_gsid) |
1151 | 1208 |
# GOTERM[[cur_gsid]] |
... | ... |
@@ -1162,7 +1219,7 @@ GeneTonic <- function(dds, |
1162 | 1219 |
# )) |
1163 | 1220 |
cur_gsid <- res_enrich$gs_id[match(input$emap_visnet_selected, res_enrich$gs_description)] |
1164 | 1221 |
validate(need(!is.na(cur_gsid), |
1165 |
- message = "Please select a gene set from the Enrichment Map." |
|
1222 |
+ message = "Please select a gene set from the Enrichment Map." |
|
1166 | 1223 |
)) |
1167 | 1224 |
|
1168 | 1225 |
|
... | ... |
@@ -1206,7 +1263,8 @@ GeneTonic <- function(dds, |
1206 | 1263 |
res_enrich = res_enrich, |
1207 | 1264 |
res_de = res_de, |
1208 | 1265 |
annotation_obj = annotation_obj, |
1209 |
- n_gs = input$n_genesets_distill) |
|
1266 |
+ n_gs = input$n_genesets_distill |
|
1267 |
+ ) |
|
1210 | 1268 |
return(distillat) |
1211 | 1269 |
}) |
1212 | 1270 |
|
... | ... |
@@ -1216,13 +1274,14 @@ GeneTonic <- function(dds, |
1216 | 1274 |
# TODO: reorder the columns from the distilled table |
1217 | 1275 |
|
1218 | 1276 |
DT::datatable( |
1219 |
- dist_table[,1:4], |
|
1277 |
+ dist_table[, 1:4], |
|
1220 | 1278 |
selection = "single", |
1221 | 1279 |
rownames = FALSE, |
1222 | 1280 |
options = list( |
1223 | 1281 |
pageLength = 50, |
1224 | 1282 |
scrollX = TRUE, |
1225 |
- scrollY = "400px") |
|
1283 |
+ scrollY = "400px" |
|
1284 |
+ ) |
|
1226 | 1285 |
) |
1227 | 1286 |
}) |
1228 | 1287 |
|
... | ... |
@@ -1253,18 +1312,17 @@ GeneTonic <- function(dds, |
1253 | 1312 |
s <- input$dt_distill_rows_selected |
1254 | 1313 |
|
1255 | 1314 |
validate(need(length(s) > 0, |
1256 |
- message = "Please select a meta-geneset from the table" |
|
1315 |
+ message = "Please select a meta-geneset from the table" |
|
1257 | 1316 |
)) |
1258 | 1317 |
|
1259 |
- selrow <- dist_table[s,]$metags_msgs |
|
1318 |
+ selrow <- dist_table[s, ]$metags_msgs |
|
1260 | 1319 |
|
1261 |
- sel_genes <- strsplit(dist_table[s,]$metags_genes, ",")[[1]] |
|
1320 |
+ sel_genes <- strsplit(dist_table[s, ]$metags_genes, ",")[[1]] |
|
1262 | 1321 |
# message(length(sel_genes)) |
1263 | 1322 |
sel_genes_id <- annotation_obj$gene_id[match(sel_genes, annotation_obj$gene_name)] |
1264 | 1323 |
# message(length(sel_genes_id)) |
1265 | 1324 |
|
1266 | 1325 |
if (!is.null(input$exp_condition)) { |
1267 |
- |
|
1268 | 1326 |
gs_heatmap( |
1269 | 1327 |
myvst, |
1270 | 1328 |
res_de, |
... | ... |
@@ -1279,7 +1337,6 @@ GeneTonic <- function(dds, |
1279 | 1337 |
scale_row = TRUE, |
1280 | 1338 |
anno_col_info = input$exp_condition, |
1281 | 1339 |
plot_title = selrow |
1282 |
- |
|
1283 | 1340 |
) |
1284 | 1341 |
} else { |
1285 | 1342 |
gs_heatmap( |
... | ... |
@@ -1314,12 +1371,15 @@ GeneTonic <- function(dds, |
1314 | 1371 |
V(ig)$color.border <- "black" |
1315 | 1372 |
|
1316 | 1373 |
visNetwork::visIgraph(ig) %>% |
1317 |
- visOptions(highlightNearest = list(enabled = TRUE, |
|
1318 |
- degree = 1, |
|
1319 |
- hover = TRUE), |
|
1320 |
- nodesIdSelection = TRUE, |
|
1321 |
- selectedBy = "membership") |
|
1322 |
- |
|
1374 |
+ visOptions( |
|
1375 |
+ highlightNearest = list( |
|
1376 |
+ enabled = TRUE, |
|
1377 |
+ degree = 1, |
|
1378 |
+ hover = TRUE |
|
1379 |
+ ), |
|
1380 |
+ nodesIdSelection = TRUE, |
|
1381 |
+ selectedBy = "membership" |
|
1382 |
+ ) |
|
1323 | 1383 |
}) |
1324 | 1384 |
|
1325 | 1385 |
|
... | ... |
@@ -1328,15 +1388,17 @@ GeneTonic <- function(dds, |
1328 | 1388 |
|
1329 | 1389 |
output$enriched_funcres <- renderPlot({ |
1330 | 1390 |
enhance_table(res_enrich, res_de, |
1331 |
- annotation_obj = annotation_obj, |
|
1332 |
- n_gs = input$n_genesets) |
|
1391 |
+ annotation_obj = annotation_obj, |
|
1392 |
+ n_gs = input$n_genesets |
|
1393 |
+ ) |
|
1333 | 1394 |
}) |
1334 | 1395 |
|
1335 | 1396 |
output$gs_volcano <- renderPlot({ |
1336 | 1397 |
gs_volcano( |
1337 | 1398 |
get_aggrscores(res_enrich, |
1338 |
- res_de, |
|
1339 |
- annotation_obj = annotation_obj), |
|
1399 |
+ res_de, |
|
1400 |
+ annotation_obj = annotation_obj |
|
1401 |
+ ), |
|
1340 | 1402 |
volcano_labels = input$n_genesets |
1341 | 1403 |
) |
1342 | 1404 |
}) |
... | ... |
@@ -1344,32 +1406,37 @@ GeneTonic <- function(dds, |
1344 | 1406 |
output$gs_volcano_simplified <- renderPlot({ |
1345 | 1407 |
gs_volcano( |
1346 | 1408 |
get_aggrscores(gs_simplify(res_enrich, gs_overlap = input$gs_overlap), |
1347 |
- res_de, |
|
1348 |
- annotation_obj = annotation_obj), |
|
1409 |
+ res_de, |
|
1410 |
+ annotation_obj = annotation_obj |
|
1411 |
+ ), |
|
1349 | 1412 |
volcano_labels = input$n_genesets |
1350 | 1413 |
) |
1351 | 1414 |
}) |
1352 | 1415 |
|
1353 | 1416 |
output$enriched_funcres_plotly <- renderPlotly({ |
1354 | 1417 |
ggplotly(enhance_table(res_enrich, |
1355 |
- res_de, |
|
1356 |
- annotation_obj = annotation_obj, |
|
1357 |
- n_gs = input$n_genesets)) |
|
1418 |
+ res_de, |
|
1419 |
+ annotation_obj = annotation_obj, |
|
1420 |
+ n_gs = input$n_genesets |
|
1421 |
+ )) |
|
1358 | 1422 |
}) |
1359 | 1423 |
|
1360 | 1424 |
|
1361 | 1425 |
# panel GSViz ----------------------------------------------------- |
1362 | 1426 |
|
1363 | 1427 |
gss_mat <- reactive({ |
1364 |
- gs_scores(se = myvst, |
|
1365 |
- res_de = res_de, |
|
1366 |
- res_enrich = res_enrich, |
|
1367 |
- annotation_obj = annotation_obj) |
|
1428 |
+ gs_scores( |
|
1429 |
+ se = myvst, |
|
1430 |
+ res_de = res_de, |
|
1431 |
+ res_enrich = res_enrich, |
|
1432 |
+ annotation_obj = annotation_obj |
|
1433 |
+ ) |
|
1368 | 1434 |
}) |
1369 | 1435 |
output$gsscores_heatmap <- renderPlot({ |
1370 | 1436 |
gs_scoresheat( |
1371 | 1437 |
gss_mat(), |
1372 |
- n_gs = input$n_genesets) |
|
1438 |
+ n_gs = input$n_genesets |
|
1439 |
+ ) |
|
1373 | 1440 |
}) |
1374 | 1441 |
|
1375 | 1442 |
output$alluvial_genesets <- renderPlotly({ |
... | ... |
@@ -1377,38 +1444,51 @@ GeneTonic <- function(dds, |
1377 | 1444 |
}) |
1378 | 1445 |
|
1379 | 1446 |
output$mds_genesets <- renderPlot({ |
1380 |
- gs_mds(res_enrich, res_de, annotation_obj, mds_colorby = "z_score", |
|
1381 |
- mds_labels = input$n_genesets) |
|
1447 |
+ gs_mds(res_enrich, res_de, annotation_obj, |
|
1448 |
+ mds_colorby = "z_score", |
|
1449 |
+ mds_labels = input$n_genesets |
|
1450 |
+ ) |
|
1382 | 1451 |
}) |
1383 | 1452 |
|
1384 | 1453 |
output$gs_summaryheat <- renderPlot({ |
1385 | 1454 |
gs_summary_heat(res_enrich, res_de, annotation_obj, |
1386 |
- n_gs = input$n_genesets) |
|
1455 |
+ n_gs = input$n_genesets |
|
1456 |
+ ) |
|
1387 | 1457 |
}) |
1388 | 1458 |
|
1389 | 1459 |
output$gs_summaryoverview <- renderPlot({ |
1390 |
- |