-1.6.6.dev15+gd9f20b3
+1.7.2.dev0+g8abf70a.d20240415
Why do we need a better way to visualize the gene set enrichment analysis result?ΒΆ
Traditionally, we have to plot lots of barplot or dotplot to visualize the gene set enrichment analysis. For example:
-
What if we had lots of cell types and performed gene set enrichment analysis for each cell types? It is not a good idea to plot lots of barplot or dotplot in the manuscript.
In this case, we can merge all the enriched result into one matrix and plot a dotHeatmap using PyComplexHeatmap
PlotΒΆ<
-[13]:
+[9]:
left_ha = HeatmapAnnotation(
@@ -1151,7 +1151,7 @@ In this example, we used two different kinds of markers and cmap to indic
How to select marker:ΒΆ
-
+
diff --git a/docs/build/html/notebooks/gene_enrichment_analysis.ipynb b/docs/build/html/notebooks/gene_enrichment_analysis.ipynb
index 7b6fb578..b88308e1 100644
--- a/docs/build/html/notebooks/gene_enrichment_analysis.ipynb
+++ b/docs/build/html/notebooks/gene_enrichment_analysis.ipynb
@@ -20,7 +20,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "1.6.6.dev15+gd9f20b3\n"
+ "1.7.2.dev0+g8abf70a.d20240415\n"
]
}
],
@@ -966,7 +966,7 @@
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": 9,
"id": "8683f2d4-cea6-445f-ae32-cbfdb835b2ee",
"metadata": {
"tags": []
diff --git a/docs/build/html/notebooks/get_started.html b/docs/build/html/notebooks/get_started.html
index f3f8152d..7a5f4878 100644
--- a/docs/build/html/notebooks/get_started.html
+++ b/docs/build/html/notebooks/get_started.html
@@ -4,7 +4,7 @@
-
1. Import packages — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ 1. Import packages — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -18,7 +18,7 @@
-
+
diff --git a/docs/build/html/notebooks/kwargs.html b/docs/build/html/notebooks/kwargs.html
index eedb5901..4ace87e6 100644
--- a/docs/build/html/notebooks/kwargs.html
+++ b/docs/build/html/notebooks/kwargs.html
@@ -4,7 +4,7 @@
- label_kws, xticklabels_kws and yticklabels_kws: Modifying the heatmap annotations labels and xticklabels, yticklabels — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ label_kws, xticklabels_kws and yticklabels_kws: Modifying the heatmap annotations labels and xticklabels, yticklabels — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -18,7 +18,7 @@
-
+
@@ -587,7 +587,7 @@ Control gap & pad in heatmap
+
hgap and wgap for HeatmapAnnotationΒΆ
control the gap between two rows/columns of column annotations (axis=1) or row annotations (axis=0), unit is mm
diff --git a/docs/build/html/notebooks/oncoPrint.html b/docs/build/html/notebooks/oncoPrint.html
index f365ab9a..44931732 100644
--- a/docs/build/html/notebooks/oncoPrint.html
+++ b/docs/build/html/notebooks/oncoPrint.html
@@ -4,7 +4,7 @@
- oncoPrint: visualizing TCGA Lung Adenocarcinoma Carcinoma Variants Dataset — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ oncoPrint: visualizing TCGA Lung Adenocarcinoma Carcinoma Variants Dataset — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -18,7 +18,7 @@
-
+
diff --git a/docs/build/html/notebooks/oncoPrint2.html b/docs/build/html/notebooks/oncoPrint2.html
index c1858cf2..7951afc5 100644
--- a/docs/build/html/notebooks/oncoPrint2.html
+++ b/docs/build/html/notebooks/oncoPrint2.html
@@ -4,7 +4,7 @@
- Visualizing categorical variables using oncoPrint — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ Visualizing categorical variables using oncoPrint — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -18,7 +18,7 @@
-
+
diff --git a/docs/build/html/notebooks/single_cell_methylation.html b/docs/build/html/notebooks/single_cell_methylation.html
index f3e9fcf6..c17c827c 100644
--- a/docs/build/html/notebooks/single_cell_methylation.html
+++ b/docs/build/html/notebooks/single_cell_methylation.html
@@ -4,7 +4,7 @@
- Visualizing Single Cell DNA Methylation Data (Loyfer2023) — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ Visualizing Single Cell DNA Methylation Data (Loyfer2023) — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -18,7 +18,7 @@
-
+
diff --git a/docs/build/html/notebooks/test_add_anno_img.html b/docs/build/html/notebooks/test_add_anno_img.html
index 046fc16a..f87026aa 100644
--- a/docs/build/html/notebooks/test_add_anno_img.html
+++ b/docs/build/html/notebooks/test_add_anno_img.html
@@ -4,7 +4,7 @@
- <no title> — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ <no title> — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -18,7 +18,7 @@
-
+
diff --git a/docs/build/html/oncoPrint.html b/docs/build/html/oncoPrint.html
index 71f77c50..dbc9441c 100644
--- a/docs/build/html/oncoPrint.html
+++ b/docs/build/html/oncoPrint.html
@@ -4,7 +4,7 @@
- oncoPrint — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ oncoPrint — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -17,7 +17,7 @@
-
+
diff --git a/docs/build/html/py-modindex.html b/docs/build/html/py-modindex.html
index 835d8bb0..6bfec726 100644
--- a/docs/build/html/py-modindex.html
+++ b/docs/build/html/py-modindex.html
@@ -3,7 +3,7 @@
- Python Module Index — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ Python Module Index — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -16,7 +16,7 @@
-
+
diff --git a/docs/build/html/search.html b/docs/build/html/search.html
index b239271f..c67885b0 100644
--- a/docs/build/html/search.html
+++ b/docs/build/html/search.html
@@ -3,7 +3,7 @@
- Search — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ Search — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -17,7 +17,7 @@
-
+
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index e391b40f..9354eff2 100644
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/docs/build/html/setup.html b/docs/build/html/setup.html
index 7f183de5..344f5c9a 100644
--- a/docs/build/html/setup.html
+++ b/docs/build/html/setup.html
@@ -4,7 +4,7 @@
- setup module — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ setup module — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -17,7 +17,7 @@
-
+
diff --git a/notebooks/gene_enrichment_analysis.ipynb b/notebooks/gene_enrichment_analysis.ipynb
index 7b6fb578..b88308e1 100644
--- a/notebooks/gene_enrichment_analysis.ipynb
+++ b/notebooks/gene_enrichment_analysis.ipynb
@@ -20,7 +20,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "1.6.6.dev15+gd9f20b3\n"
+ "1.7.2.dev0+g8abf70a.d20240415\n"
]
}
],
@@ -966,7 +966,7 @@
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": 9,
"id": "8683f2d4-cea6-445f-ae32-cbfdb835b2ee",
"metadata": {
"tags": []
[13]:
+[9]:
left_ha = HeatmapAnnotation(
@@ -1151,7 +1151,7 @@ In this example, we used two different kinds of markers and cmap to indic
How to select marker:ΒΆ
-
+
diff --git a/docs/build/html/notebooks/gene_enrichment_analysis.ipynb b/docs/build/html/notebooks/gene_enrichment_analysis.ipynb
index 7b6fb578..b88308e1 100644
--- a/docs/build/html/notebooks/gene_enrichment_analysis.ipynb
+++ b/docs/build/html/notebooks/gene_enrichment_analysis.ipynb
@@ -20,7 +20,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "1.6.6.dev15+gd9f20b3\n"
+ "1.7.2.dev0+g8abf70a.d20240415\n"
]
}
],
@@ -966,7 +966,7 @@
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": 9,
"id": "8683f2d4-cea6-445f-ae32-cbfdb835b2ee",
"metadata": {
"tags": []
diff --git a/docs/build/html/notebooks/get_started.html b/docs/build/html/notebooks/get_started.html
index f3f8152d..7a5f4878 100644
--- a/docs/build/html/notebooks/get_started.html
+++ b/docs/build/html/notebooks/get_started.html
@@ -4,7 +4,7 @@
-
1. Import packages — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ 1. Import packages — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -18,7 +18,7 @@
-
+
diff --git a/docs/build/html/notebooks/kwargs.html b/docs/build/html/notebooks/kwargs.html
index eedb5901..4ace87e6 100644
--- a/docs/build/html/notebooks/kwargs.html
+++ b/docs/build/html/notebooks/kwargs.html
@@ -4,7 +4,7 @@
- label_kws, xticklabels_kws and yticklabels_kws: Modifying the heatmap annotations labels and xticklabels, yticklabels — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ label_kws, xticklabels_kws and yticklabels_kws: Modifying the heatmap annotations labels and xticklabels, yticklabels — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -18,7 +18,7 @@
-
+
@@ -587,7 +587,7 @@ Control gap & pad in heatmap
+
hgap and wgap for HeatmapAnnotationΒΆ
control the gap between two rows/columns of column annotations (axis=1) or row annotations (axis=0), unit is mm
diff --git a/docs/build/html/notebooks/oncoPrint.html b/docs/build/html/notebooks/oncoPrint.html
index f365ab9a..44931732 100644
--- a/docs/build/html/notebooks/oncoPrint.html
+++ b/docs/build/html/notebooks/oncoPrint.html
@@ -4,7 +4,7 @@
- oncoPrint: visualizing TCGA Lung Adenocarcinoma Carcinoma Variants Dataset — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ oncoPrint: visualizing TCGA Lung Adenocarcinoma Carcinoma Variants Dataset — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -18,7 +18,7 @@
-
+
diff --git a/docs/build/html/notebooks/oncoPrint2.html b/docs/build/html/notebooks/oncoPrint2.html
index c1858cf2..7951afc5 100644
--- a/docs/build/html/notebooks/oncoPrint2.html
+++ b/docs/build/html/notebooks/oncoPrint2.html
@@ -4,7 +4,7 @@
- Visualizing categorical variables using oncoPrint — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ Visualizing categorical variables using oncoPrint — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -18,7 +18,7 @@
-
+
diff --git a/docs/build/html/notebooks/single_cell_methylation.html b/docs/build/html/notebooks/single_cell_methylation.html
index f3e9fcf6..c17c827c 100644
--- a/docs/build/html/notebooks/single_cell_methylation.html
+++ b/docs/build/html/notebooks/single_cell_methylation.html
@@ -4,7 +4,7 @@
- Visualizing Single Cell DNA Methylation Data (Loyfer2023) — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ Visualizing Single Cell DNA Methylation Data (Loyfer2023) — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -18,7 +18,7 @@
-
+
diff --git a/docs/build/html/notebooks/test_add_anno_img.html b/docs/build/html/notebooks/test_add_anno_img.html
index 046fc16a..f87026aa 100644
--- a/docs/build/html/notebooks/test_add_anno_img.html
+++ b/docs/build/html/notebooks/test_add_anno_img.html
@@ -4,7 +4,7 @@
- <no title> — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ <no title> — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -18,7 +18,7 @@
-
+
diff --git a/docs/build/html/oncoPrint.html b/docs/build/html/oncoPrint.html
index 71f77c50..dbc9441c 100644
--- a/docs/build/html/oncoPrint.html
+++ b/docs/build/html/oncoPrint.html
@@ -4,7 +4,7 @@
- oncoPrint — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ oncoPrint — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -17,7 +17,7 @@
-
+
diff --git a/docs/build/html/py-modindex.html b/docs/build/html/py-modindex.html
index 835d8bb0..6bfec726 100644
--- a/docs/build/html/py-modindex.html
+++ b/docs/build/html/py-modindex.html
@@ -3,7 +3,7 @@
- Python Module Index — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ Python Module Index — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -16,7 +16,7 @@
-
+
diff --git a/docs/build/html/search.html b/docs/build/html/search.html
index b239271f..c67885b0 100644
--- a/docs/build/html/search.html
+++ b/docs/build/html/search.html
@@ -3,7 +3,7 @@
- Search — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ Search — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -17,7 +17,7 @@
-
+
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index e391b40f..9354eff2 100644
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/docs/build/html/setup.html b/docs/build/html/setup.html
index 7f183de5..344f5c9a 100644
--- a/docs/build/html/setup.html
+++ b/docs/build/html/setup.html
@@ -4,7 +4,7 @@
- setup module — PyComplexHeatmap 1.6.6.dev15+gd9f20b3 documentation
+ setup module — PyComplexHeatmap 1.7.2.dev0+g8abf70a.d20240415 documentation
@@ -17,7 +17,7 @@
-
+
diff --git a/notebooks/gene_enrichment_analysis.ipynb b/notebooks/gene_enrichment_analysis.ipynb
index 7b6fb578..b88308e1 100644
--- a/notebooks/gene_enrichment_analysis.ipynb
+++ b/notebooks/gene_enrichment_analysis.ipynb
@@ -20,7 +20,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "1.6.6.dev15+gd9f20b3\n"
+ "1.7.2.dev0+g8abf70a.d20240415\n"
]
}
],
@@ -966,7 +966,7 @@
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": 9,
"id": "8683f2d4-cea6-445f-ae32-cbfdb835b2ee",
"metadata": {
"tags": []