diff --git a/.nojekyll b/.nojekyll index 704375f..07ef76b 100644 --- a/.nojekyll +++ b/.nojekyll @@ -1 +1 @@ -3e9a1faa \ No newline at end of file +6e8e0767 \ No newline at end of file diff --git a/panels.html b/panels.html index cb24f1b..4e66494 100644 --- a/panels.html +++ b/panels.html @@ -664,6 +664,53 @@

DETable

The DETable panel class.
+
+ +
+
+
+
library(iSEE)
+library(iSEEde)
+library(airway)
+library(DESeq2)
+
+# Example data ----
+
+data("airway")
+airway$dex <- relevel(airway$dex, "untrt")
+
+dds <- DESeqDataSet(airway, ~ 0 + dex + cell)
+
+dds <- DESeq(dds)
+res_deseq2 <- results(dds, contrast = list("dextrt", "dexuntrt"))
+
+# iSEE / iSEEde ---
+
+airway <- embedContrastResults(res_deseq2, airway, name = "dex: trt vs untrt")
+
+app <- iSEE(airway, initial = list(
+  DETable(
+    PanelWidth = 12L,
+    ContrastName="dex: trt vs untrt",
+    RoundDigits = TRUE
+  )
+))
+
+if (interactive()) {
+  shiny::runApp(app)
+}
+
+
+
+

LogFCLogFCPlot

@@ -674,6 +721,68 @@

LogFCLogFCPlot

The LogFCLogFCPlot panel class.
+
+ +
+
+
+
library("iSEEde")
+library("airway")
+library("edgeR")
+library("DESeq2")
+library("iSEE")
+
+# Example data ----
+
+data("airway")
+airway$dex <- relevel(airway$dex, "untrt")
+
+# DESeq2 ----
+
+dds <- DESeqDataSet(airway, ~ 0 + dex + cell)
+
+dds <- DESeq(dds)
+res_deseq2 <- results(dds, contrast = list("dextrt", "dexuntrt"))
+
+airway <- embedContrastResults(res_deseq2, airway, name = "DESeq2")
+
+# edgeR ----
+
+design <- model.matrix(~ 0 + dex + cell, data = colData(airway))
+
+fit <- glmFit(airway, design, dispersion = 0.1)
+lrt <- glmLRT(fit, contrast = c(-1, 1, 0, 0, 0))
+res_edger <- topTags(lrt, n = Inf)
+
+airway <- embedContrastResults(res_edger, airway, name = "edgeR")
+
+# iSEE / iSEEde ---
+
+airway <- registerAppOptions(airway, factor.maxlevels = 30, color.maxlevels = 30)
+
+app <- iSEE(airway, initial = list(
+  LogFCLogFCPlot(
+    ContrastNameX = "DESeq2", ContrastNameY = "edgeR",
+    ColorBy = "Row data",
+    ColorByRowData = "gene_biotype",
+    PanelWidth = 12L)
+))
+
+if (interactive()) {
+  shiny::runApp(app)
+}
+
+
+
+

MAPlot

@@ -684,6 +793,55 @@

MAPlot

The MAPlot panel class.
+
+ +
+
+
+
library("iSEEde")
+library("airway")
+library("DESeq2")
+library("iSEE")
+
+# Example data ----
+
+data("airway")
+airway$dex <- relevel(airway$dex, "untrt")
+rowData(airway)$seq_strand <- factor(rowData(airway)$seq_strand)
+
+dds <- DESeqDataSet(airway, ~ 0 + dex + cell)
+
+dds <- DESeq(dds)
+res_deseq2 <- results(dds, contrast = list("dextrt", "dexuntrt"))
+
+# iSEE / iSEEde ---
+
+airway <- embedContrastResults(res_deseq2, airway, name = "dex: trt vs untrt")
+
+app <- iSEE(airway, initial = list(
+  MAPlot(
+    PanelWidth = 12L,
+    ContrastName="dex: trt vs untrt",
+    ColorBy = "Row data",
+    ColorByRowData = "seq_strand"
+  )
+))
+
+if (interactive()) {
+  shiny::runApp(app)
+}
+
+
+
+

VolcanoPlot

@@ -694,6 +852,55 @@

VolcanoPlot

The VolcanoPlot panel class.
+
+ +
+
+
+
library(iSEE)
+library(iSEEde)
+library(airway)
+library(DESeq2)
+
+# Example data ----
+
+data("airway")
+airway$dex <- relevel(airway$dex, "untrt")
+rowData(airway)$seq_strand <- factor(rowData(airway)$seq_strand)
+
+dds <- DESeqDataSet(airway, ~ 0 + dex + cell)
+
+dds <- DESeq(dds)
+res_deseq2 <- results(dds, contrast = list("dextrt", "dexuntrt"))
+
+# iSEE / iSEEde ---
+
+airway <- embedContrastResults(res_deseq2, airway, name = "dex: trt vs untrt")
+
+app <- iSEE(airway, initial = list(
+  VolcanoPlot(
+    PanelWidth = 12L,
+    ContrastName="dex: trt vs untrt",
+    ColorBy = "Row data",
+    ColorByRowData = "seq_strand"
+  )
+))
+
+if (interactive()) {
+  shiny::runApp(app)
+}
+
+
+
+
@@ -707,6 +914,42 @@

ReducedDimensionHe
The ReducedDimensionHexPlot panel class.
+
+ +
+
+
+
library(iSEE)
+library(iSEEhex)
+library(scRNAseq)
+library(scater)
+
+# Example data ----
+sce <- ReprocessedAllenData(assays="tophat_counts")
+
+sce <- logNormCounts(sce, exprs_values="tophat_counts")
+
+sce <- runPCA(sce, ncomponents=4)
+
+# launch the app itself ----
+
+if (interactive()) {
+  iSEE(sce, initial=list(
+    ReducedDimensionHexPlot(PanelWidth = 12L, BinResolution=50)
+  ))
+}
+
+
+
+
diff --git a/search.json b/search.json index a3fb2d1..f17d7b8 100644 --- a/search.json +++ b/search.json @@ -228,14 +228,14 @@ "href": "panels.html#iseede", "title": "Panels", "section": "iSEEde", - "text": "iSEEde\n\nDETable\nBrowse and filter any table of differential expression results embedded in a SummarizedExperiment object.\n\n\n\nThe DETable panel class.\n\n\n\n\nLogFCLogFCPlot\nVisualise the log-transformed fold-changes of any two differential expression contrasts embedded in a SummarizedExperiment object.\n\n\n\nThe LogFCLogFCPlot panel class.\n\n\n\n\nMAPlot\nVisualise the M and A values of any differential expression contrast embedded in a SummarizedExperiment object.\n\n\n\nThe MAPlot panel class.\n\n\n\n\nVolcanoPlot\nVisualise the P values and log-transformed fold-changes of any differential expression contrast embedded in a SummarizedExperiment object.\n\n\n\nThe VolcanoPlot panel class." + "text": "iSEEde\n\nDETable\nBrowse and filter any table of differential expression results embedded in a SummarizedExperiment object.\n\n\n\nThe DETable panel class.\n\n\n\n\n\n\n\n\nReproduce This Output\n\n\n\n\n\n\nlibrary(iSEE)\nlibrary(iSEEde)\nlibrary(airway)\nlibrary(DESeq2)\n\n# Example data ----\n\ndata(\"airway\")\nairway$dex <- relevel(airway$dex, \"untrt\")\n\ndds <- DESeqDataSet(airway, ~ 0 + dex + cell)\n\ndds <- DESeq(dds)\nres_deseq2 <- results(dds, contrast = list(\"dextrt\", \"dexuntrt\"))\n\n# iSEE / iSEEde ---\n\nairway <- embedContrastResults(res_deseq2, airway, name = \"dex: trt vs untrt\")\n\napp <- iSEE(airway, initial = list(\n DETable(\n PanelWidth = 12L,\n ContrastName=\"dex: trt vs untrt\",\n RoundDigits = TRUE\n )\n))\n\nif (interactive()) {\n shiny::runApp(app)\n}\n\n\n\n\n\n\nLogFCLogFCPlot\nVisualise the log-transformed fold-changes of any two differential expression contrasts embedded in a SummarizedExperiment object.\n\n\n\nThe LogFCLogFCPlot panel class.\n\n\n\n\n\n\n\n\nReproduce This Output\n\n\n\n\n\n\nlibrary(\"iSEEde\")\nlibrary(\"airway\")\nlibrary(\"edgeR\")\nlibrary(\"DESeq2\")\nlibrary(\"iSEE\")\n\n# Example data ----\n\ndata(\"airway\")\nairway$dex <- relevel(airway$dex, \"untrt\")\n\n# DESeq2 ----\n\ndds <- DESeqDataSet(airway, ~ 0 + dex + cell)\n\ndds <- DESeq(dds)\nres_deseq2 <- results(dds, contrast = list(\"dextrt\", \"dexuntrt\"))\n\nairway <- embedContrastResults(res_deseq2, airway, name = \"DESeq2\")\n\n# edgeR ----\n\ndesign <- model.matrix(~ 0 + dex + cell, data = colData(airway))\n\nfit <- glmFit(airway, design, dispersion = 0.1)\nlrt <- glmLRT(fit, contrast = c(-1, 1, 0, 0, 0))\nres_edger <- topTags(lrt, n = Inf)\n\nairway <- embedContrastResults(res_edger, airway, name = \"edgeR\")\n\n# iSEE / iSEEde ---\n\nairway <- registerAppOptions(airway, factor.maxlevels = 30, color.maxlevels = 30)\n\napp <- iSEE(airway, initial = list(\n LogFCLogFCPlot(\n ContrastNameX = \"DESeq2\", ContrastNameY = \"edgeR\",\n ColorBy = \"Row data\",\n ColorByRowData = \"gene_biotype\",\n PanelWidth = 12L)\n))\n\nif (interactive()) {\n shiny::runApp(app)\n}\n\n\n\n\n\n\nMAPlot\nVisualise the M and A values of any differential expression contrast embedded in a SummarizedExperiment object.\n\n\n\nThe MAPlot panel class.\n\n\n\n\n\n\n\n\nReproduce This Output\n\n\n\n\n\n\nlibrary(\"iSEEde\")\nlibrary(\"airway\")\nlibrary(\"DESeq2\")\nlibrary(\"iSEE\")\n\n# Example data ----\n\ndata(\"airway\")\nairway$dex <- relevel(airway$dex, \"untrt\")\nrowData(airway)$seq_strand <- factor(rowData(airway)$seq_strand)\n\ndds <- DESeqDataSet(airway, ~ 0 + dex + cell)\n\ndds <- DESeq(dds)\nres_deseq2 <- results(dds, contrast = list(\"dextrt\", \"dexuntrt\"))\n\n# iSEE / iSEEde ---\n\nairway <- embedContrastResults(res_deseq2, airway, name = \"dex: trt vs untrt\")\n\napp <- iSEE(airway, initial = list(\n MAPlot(\n PanelWidth = 12L,\n ContrastName=\"dex: trt vs untrt\",\n ColorBy = \"Row data\",\n ColorByRowData = \"seq_strand\"\n )\n))\n\nif (interactive()) {\n shiny::runApp(app)\n}\n\n\n\n\n\n\nVolcanoPlot\nVisualise the P values and log-transformed fold-changes of any differential expression contrast embedded in a SummarizedExperiment object.\n\n\n\nThe VolcanoPlot panel class.\n\n\n\n\n\n\n\n\nReproduce This Output\n\n\n\n\n\n\nlibrary(iSEE)\nlibrary(iSEEde)\nlibrary(airway)\nlibrary(DESeq2)\n\n# Example data ----\n\ndata(\"airway\")\nairway$dex <- relevel(airway$dex, \"untrt\")\nrowData(airway)$seq_strand <- factor(rowData(airway)$seq_strand)\n\ndds <- DESeqDataSet(airway, ~ 0 + dex + cell)\n\ndds <- DESeq(dds)\nres_deseq2 <- results(dds, contrast = list(\"dextrt\", \"dexuntrt\"))\n\n# iSEE / iSEEde ---\n\nairway <- embedContrastResults(res_deseq2, airway, name = \"dex: trt vs untrt\")\n\napp <- iSEE(airway, initial = list(\n VolcanoPlot(\n PanelWidth = 12L,\n ContrastName=\"dex: trt vs untrt\",\n ColorBy = \"Row data\",\n ColorByRowData = \"seq_strand\"\n )\n))\n\nif (interactive()) {\n shiny::runApp(app)\n}" }, { "objectID": "panels.html#iseehex", "href": "panels.html#iseehex", "title": "Panels", "section": "iSEEhex", - "text": "iSEEhex\n\nReducedDimensionHexPlot\nSame as ReducedDimensionPlot but summarised using hexagonal bins.\n\n\n\nThe ReducedDimensionHexPlot panel class." + "text": "iSEEhex\n\nReducedDimensionHexPlot\nSame as ReducedDimensionPlot but summarised using hexagonal bins.\n\n\n\nThe ReducedDimensionHexPlot panel class.\n\n\n\n\n\n\n\n\nReproduce This Output\n\n\n\n\n\n\nlibrary(iSEE)\nlibrary(iSEEhex)\nlibrary(scRNAseq)\nlibrary(scater)\n\n# Example data ----\nsce <- ReprocessedAllenData(assays=\"tophat_counts\")\n\nsce <- logNormCounts(sce, exprs_values=\"tophat_counts\")\n\nsce <- runPCA(sce, ncomponents=4)\n\n# launch the app itself ----\n\nif (interactive()) {\n iSEE(sce, initial=list(\n ReducedDimensionHexPlot(PanelWidth = 12L, BinResolution=50)\n ))\n}" }, { "objectID": "index.html", diff --git a/sitemap.xml b/sitemap.xml index 6dd9e15..f03be29 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -2,34 +2,34 @@ https://isee.github.io/videos.html - 2024-10-09T08:18:21.413Z + 2024-10-09T10:09:31.124Z https://isee.github.io/about.html - 2024-10-09T08:18:19.865Z + 2024-10-09T10:09:29.820Z https://isee.github.io/apps.html - 2024-10-09T08:18:17.422Z + 2024-10-09T10:09:27.482Z https://isee.github.io/dashboard.html - 2024-10-09T08:18:16.008Z + 2024-10-09T10:09:26.024Z https://isee.github.io/panels.html - 2024-10-09T08:18:15.300Z + 2024-10-09T10:09:25.174Z https://isee.github.io/index.html - 2024-10-09T08:18:16.600Z + 2024-10-09T10:09:26.615Z https://isee.github.io/install.html - 2024-10-09T08:18:19.254Z + 2024-10-09T10:09:29.273Z https://isee.github.io/resources.html - 2024-10-09T08:18:20.754Z + 2024-10-09T10:09:30.572Z