diff --git a/articles/workshop_isee_extension.html b/articles/workshop_isee_extension.html index 8bc07db..df6b208 100644 --- a/articles/workshop_isee_extension.html +++ b/articles/workshop_isee_extension.html @@ -77,7 +77,7 @@

Writing iSEE extensions

Kevin -Rue-Albrecht1,Federico Marini2, Charlotte Soneson3 +Rue-Albrecht1, Federico Marini2, Charlotte Soneson3

@@ -306,8 +306,9 @@

Getting started with iSEE 
 library(iSEE)
+library(shiny)
 app <- iSEE(sce)
-runApp(app, launch.browser = TRUE)
+runApp(app, launch.browser = TRUE)

Screenshot of iSEE app.
Screenshot of iSEE app.
@@ -415,7 +416,7 @@

Core iSEE functionality 
 app <- iSEE(sce)
-runApp(app, launch.browser = TRUE)
+runApp(app, launch.browser = TRUE)
Screenshot of iSEE app.
Screenshot of iSEE app.
@@ -441,7 +442,7 @@

Core iSEE functionality# Settings for Reduced dimension plot 1 ################################################################################ -initial[["ReducedDimensionPlot1"]] <- new("ReducedDimensionPlot", Type = "PCA", XAxis = 1L, YAxis = 2L, +initial[["ReducedDimensionPlot1"]] <- new("ReducedDimensionPlot", Type = "PCA", XAxis = 1L, YAxis = 2L, FacetRowByColData = "driver_1_s", FacetColumnByColData = "driver_1_s", ColorByColumnData = "NREADS", ColorByFeatureNameAssay = "logcounts", ColorBySampleNameColor = "#FF0000", ShapeByColumnData = "driver_1_s", @@ -470,7 +471,7 @@

Core iSEE functionality# Settings for Feature assay plot 1 ################################################################################ -initial[["FeatureAssayPlot1"]] <- new("FeatureAssayPlot", Assay = "logcounts", XAxis = "None", +initial[["FeatureAssayPlot1"]] <- new("FeatureAssayPlot", Assay = "logcounts", XAxis = "None", XAxisColumnData = "NREADS", XAxisFeatureName = "0610007P14Rik", XAxisFeatureSource = "---", XAxisFeatureDynamicSource = FALSE, YAxisFeatureName = "0610007P14Rik", YAxisFeatureSource = "---", @@ -510,7 +511,7 @@

Core iSEE functionality 
 app <- iSEE(sce, initial = initial)
-runApp(app, launch.browser = TRUE)
+runApp(app, launch.browser = TRUE)
Screenshot of iSEE app launched in a predefined initial configuration.
Screenshot of iSEE app launched in a predefined initial configuration.
@@ -708,7 +709,7 @@

Pathway analysis 
 library("org.Hs.eg.db")
-pathways <- select(org.Hs.eg.db, keys(org.Hs.eg.db, "ENSEMBL"), c("GOALL"), keytype = "ENSEMBL")
+pathways <- select(org.Hs.eg.db, head(keys(org.Hs.eg.db, "GOALL"), 100), c("ENSEMBL"), keytype = "GOALL")
 pathways <- subset(pathways, ONTOLOGYALL == "BP")
 pathways <- unique(pathways[, c("ENSEMBL", "GOALL")])
 pathways <- merge(pathways, rowData(airway)[, c("ENSEMBL", "uniquifyFeatureNames")])
@@ -733,22 +734,22 @@ 
Pathway analysis#> Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (25.61% of the list).
 #> The order of those tied genes will be arbitrary, which may produce unexpected results.
 head(fgseaRes[order(pval), ])
-#>       pathway         pval        padj   log2err        ES      NES  size
-#>        <char>        <num>       <num>     <num>     <num>    <num> <int>
-#> 1: GO:0071294 5.864480e-07 0.002487553 0.6594444 0.8124702 2.239911    19
-#> 2: GO:0061687 1.034325e-06 0.002487553 0.6435518 0.8176539 2.198248    17
-#> 3: GO:0071280 2.768611e-06 0.004439007 0.6272567 0.7601160 2.189482    22
-#> 4: GO:0035357 5.771481e-06 0.006535683 0.6105269 0.7534512 2.189955    23
-#> 5: GO:0097501 6.947335e-06 0.006535683 0.6105269 0.8018175 2.097399    16
-#> 6: GO:0043501 8.152619e-06 0.006535683 0.5933255 0.7557131 2.157048    21
+#>       pathway       pval      padj   log2err         ES       NES  size
+#>        <char>      <num>     <num>     <num>      <num>     <num> <int>
+#> 1: GO:0006953 0.08086785 0.6105632 0.2220560  0.4207971  1.344516    36
+#> 2: GO:0008585 0.09074074 0.6105632 0.2020717  0.3246918  1.261056    94
+#> 3: GO:0022602 0.10074627 0.6105632 0.1918922  0.3846962  1.303461    45
+#> 4: GO:0002437 0.16279070 0.6105632 0.1585141 -0.3364185 -1.209283    58
+#> 5: GO:0002697 0.19527897 0.6105632 0.1446305 -0.2416966 -1.095904   307
+#> 6: GO:0006959 0.19870410 0.6105632 0.1437590 -0.2678407 -1.130609   158
 #>     leadingEdge
 #>          <list>
-#> 1: MT1X, MT....
-#> 2: MT1X, MT....
-#> 3: MT1X, MT....
-#> 4: ALOX15B,....
-#> 5: MT1X, MT....
-#> 6: TRIM63, ....
+#> 1: CD163, S.... +#> 2: INHBB, L.... +#> 3: LEP, ADA.... +#> 4: IL1RN, R.... +#> 5: RSAD2, I.... +#> 6: TSLP, WF....

Similarly to the differential expression analysis, we embed the results of the DESeq2 analysis within the airway object, this time using the @@ -815,7 +816,7 @@

Live app ClusterRows = TRUE, ClusterRowsDistance = "euclidean", AssayCenterRows = TRUE), FgseaEnrichmentPlot(PanelWidth = 12L) )) -runApp(app, launch.browser = TRUE) +runApp(app, launch.browser = TRUE)
Screenshot of iSEE app including extension panels and launched in a predefined initial configuration.
Screenshot of iSEE app including extension panels and launched in a predefined initial configuration.
@@ -919,7 +920,7 @@

Creating a constructor function ReducedDimensionHexPlot(PanelWidth = 6L), ReducedDimensionPlot(PanelWidth = 6L) )) -runApp(app, launch.browser = TRUE)

+runApp(app, launch.browser = TRUE)
Screenshot of iSEE app including a parent ReducedDimensionPlot and a ReducedDimensionHexPlot extension.
Screenshot of iSEE app including a parent ReducedDimensionPlot and a ReducedDimensionHexPlot extension.
@@ -942,7 +943,7 @@

Changing the public panel nameReducedDimensionHexPlot(PanelWidth = 6L), ReducedDimensionPlot(PanelWidth = 6L) )) -runApp(app, launch.browser = TRUE)

+runApp(app, launch.browser = TRUE)
Screenshot of iSEE app including a parent ReducedDimensionPlot and a ReducedDimensionHexPlot extension after changing the full name of the child panel.
Screenshot of iSEE app including a parent ReducedDimensionPlot and a ReducedDimensionHexPlot extension after @@ -966,7 +967,7 @@

Changing the background panel colo ReducedDimensionHexPlot(PanelWidth = 6L), ReducedDimensionPlot(PanelWidth = 6L) )) -runApp(app, launch.browser = TRUE)

+runApp(app, launch.browser = TRUE)
Screenshot of iSEE app including a parent ReducedDimensionPlot and a ReducedDimensionHexPlot extension after changing the background colour of the child panel.
Screenshot of iSEE app including a parent ReducedDimensionPlot and a ReducedDimensionHexPlot extension after @@ -994,7 +995,7 @@

Altering the user interfacesetMethod(".defineVisualSizeInterface", "ReducedDimensionHexPlot", function(x) { plot_name <- .getEncodedName(x) - tagList( + tagList( .numericInput.iSEE(x, "BinResolution", label="Bin resolution:", min=1, value=x[["BinResolution"]], step = 1) ) @@ -1004,7 +1005,7 @@

Altering the user interfaceReducedDimensionHexPlot(PanelWidth = 6L, VisualBoxOpen = TRUE, VisualChoices = "Size"), ReducedDimensionPlot(PanelWidth = 6L, VisualBoxOpen = TRUE, VisualChoices = "Size") )) -runApp(app, launch.browser = TRUE)

+runApp(app, launch.browser = TRUE)
Screenshot of iSEE app including a parent ReducedDimensionPlot and a ReducedDimensionHexPlot extension after replacing the size parameter interface in the child panel.
Screenshot of iSEE app including a parent ReducedDimensionPlot and a ReducedDimensionHexPlot extension after @@ -1041,7 +1042,7 @@

Altering the panel output ReducedDimensionHexPlot(PanelWidth = 6L, VisualBoxOpen = TRUE, VisualChoices = "Size"), ReducedDimensionPlot(PanelWidth = 6L, VisualBoxOpen = TRUE, VisualChoices = "Size") )) -runApp(app, launch.browser = TRUE)

+runApp(app, launch.browser = TRUE)
Screenshot of iSEE app including a parent ReducedDimensionPlot and a ReducedDimensionHexPlot extension after replacing the internal plotting code in the child panel.
Screenshot of iSEE app including a parent ReducedDimensionPlot and a ReducedDimensionHexPlot extension after @@ -1086,7 +1087,7 @@

Adding reactivityReducedDimensionHexPlot(PanelWidth = 6L, VisualBoxOpen = TRUE, VisualChoices = "Size"), ReducedDimensionPlot(PanelWidth = 6L) )) -runApp(app, launch.browser = TRUE)

+runApp(app, launch.browser = TRUE)
Screenshot of iSEE app including a parent ReducedDimensionPlot and a ReducedDimensionHexPlot extension after adding an observer in the child panel and using the value of the new interface element.
Screenshot of iSEE app including a parent ReducedDimensionPlot and a ReducedDimensionHexPlot extension after @@ -1149,7 +1150,7 @@

Session info#> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Etc/UTC -#> date 2024-08-01 +#> date 2024-08-02 #> pandoc 3.2 @ /usr/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── @@ -1205,10 +1206,10 @@

Session info#> doParallel 1.0.17 2022-02-07 [2] RSPM (R 4.4.0) #> dplyr 1.1.4 2023-11-17 [2] RSPM (R 4.4.0) #> DT 0.33 2024-04-04 [2] RSPM (R 4.4.0) -#> edgeR 4.3.6 2024-07-30 [2] Bioconductor 3.20 (R 4.4.1) +#> edgeR 4.3.7 2024-07-31 [2] Bioconductor 3.20 (R 4.4.1) #> ensembldb 2.29.0 2024-05-01 [2] Bioconductor 3.20 (R 4.4.0) #> evaluate 0.24.0 2024-06-10 [2] RSPM (R 4.4.0) -#> ExperimentHub 2.13.0 2024-05-01 [2] Bioconductor 3.20 (R 4.4.0) +#> ExperimentHub 2.13.1 2024-07-31 [2] Bioconductor 3.20 (R 4.4.1) #> fansi 1.0.6 2023-12-08 [2] RSPM (R 4.4.0) #> fastmap 1.2.0 2024-05-15 [2] RSPM (R 4.4.0) #> fastmatch 1.1-4 2023-08-18 [2] RSPM (R 4.4.0) @@ -1272,7 +1273,7 @@

Session info#> pkgdown 2.1.0 2024-07-06 [2] RSPM (R 4.4.0) #> png 0.1-8 2022-11-29 [2] RSPM (R 4.4.0) #> promises 1.3.0 2024-04-05 [2] RSPM (R 4.4.0) -#> ProtGenerics 1.37.0 2024-05-01 [2] Bioconductor 3.20 (R 4.4.0) +#> ProtGenerics 1.37.1 2024-07-31 [2] Bioconductor 3.20 (R 4.4.1) #> R6 2.5.1 2021-08-19 [2] RSPM (R 4.4.0) #> ragg 1.3.2 2024-05-15 [2] RSPM (R 4.4.0) #> rappdirs 0.3.3 2021-01-31 [2] RSPM (R 4.4.0) @@ -1321,7 +1322,7 @@

Session info#> vipor 0.4.7 2023-12-18 [2] RSPM (R 4.4.0) #> viridis 0.6.5 2024-01-29 [2] RSPM (R 4.4.0) #> viridisLite 0.4.2 2023-05-02 [2] RSPM (R 4.4.0) -#> withr 3.0.0 2024-01-16 [2] RSPM (R 4.4.0) +#> withr 3.0.1 2024-07-31 [2] RSPM (R 4.4.0) #> xfun 0.46 2024-07-18 [2] RSPM (R 4.4.0) #> XML 3.99-0.17 2024-06-25 [2] RSPM (R 4.4.0) #> xtable 1.8-4 2019-04-21 [2] RSPM (R 4.4.0) @@ -1329,7 +1330,7 @@

Session info#> yaml 2.3.10 2024-07-26 [2] RSPM (R 4.4.0) #> zlibbioc 1.51.1 2024-06-05 [2] Bioconductor 3.20 (R 4.4.0) #> -#> [1] /tmp/RtmpqJ7g90/temp_libpath6f454729ea0 +#> [1] /tmp/RtmpMrDwuc/temp_libpath78d51050cc9 #> [2] /usr/local/lib/R/site-library #> [3] /usr/local/lib/R/library #> @@ -1339,7 +1340,7 @@

Session infoTimings

Wallclock time spent generating the vignette.

-
#> Time difference of 1.278 mins
+
#> Time difference of 47.556 secs

diff --git a/pkgdown.yml b/pkgdown.yml index eabc1c4..b455fa1 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,7 +3,7 @@ pkgdown: 2.1.0 pkgdown_sha: ~ articles: workshop_isee_extension: workshop_isee_extension.html -last_built: 2024-08-01T09:34Z +last_built: 2024-08-02T08:41Z urls: reference: https://isee.github.io/iSEEDemoEuroBioC2024/reference article: https://isee.github.io/iSEEDemoEuroBioC2024/articles