diff --git a/README.Rmd b/README.Rmd index 6abe7b58..8221f50f 100644 --- a/README.Rmd +++ b/README.Rmd @@ -11,7 +11,7 @@ knitr::opts_chunk$set( results = "hide", message = FALSE, warning = FALSE, - fig.path = "README/README-", + fig.path = "man/figures/", fig.height = 5, fig.width = 10, fig.align = "center", @@ -57,7 +57,7 @@ if (!require("devtools", quietly = TRUE)) { devtools::install_github("zhanghao-njmu/SCP") ``` -#### Create SCP python environment +#### Create a python environment for SCP To run functions such as `RunPAGA` or `RunSCVELO`, SCP requires [conda](https://docs.conda.io/en/latest/miniconda.html) to create a separate python environment. The default environment name is `"SCP_env"`. You can specify the environment name for SCP by setting `options(SCP_env_name="new_name")` @@ -282,13 +282,13 @@ CellDimPlot( CellDimPlot3D(srt = pancreas_sub, group.by = "SubCellType") ``` -![CellDimPlot3D](README/README-CellDimPlot3D-1.png) +![CellDimPlot3D](man/figures/CellDimPlot3D-1.png) ```{r FeatureDimPlot3D,eval=FALSE} FeatureDimPlot3D(srt = pancreas_sub, features = c("Sox9", "Neurog3", "Fev", "Rbp4")) ``` -![FeatureDimPlot3D](README/README-FeatureDimPlot3D-1.png) +![FeatureDimPlot3D](man/figures/FeatureDimPlot3D-1.png) ### Integration pipeline @@ -330,7 +330,7 @@ grob <- gtable_add_grob(grob, legend, t = 1, l = min(grob$layout[grepl(pattern = panel_fix(grob, height = 2) ``` -![Integration-all](README/README-Integration-all.png) +![Integration-all](man/figures/Integration-all.png) ### Cell projection between single-cell datasets @@ -540,10 +540,10 @@ if (interactive()) { } ``` -![SCExplorer1](README/README-SCExplorer-1.png) ![SCExplorer2](README/README-SCExplorer-2.png) +![SCExplorer1](man/figures/SCExplorer-1.png) ![SCExplorer2](man/figures/SCExplorer-2.png) ### Other visualization examples -[**CellDimPlot**](https://zhanghao-njmu.github.io/SCP/reference/CellDimPlot.html)![Example1](README/README-Example-1.jpg) [**CellStatPlot**](https://zhanghao-njmu.github.io/SCP/reference/CellStatPlot.html)![Example2](README/README-Example-2.jpg) [**FeatureStatPlot**](https://zhanghao-njmu.github.io/SCP/reference/FeatureStatPlot.html)![Example3](README/README-Example-3.jpg) [**GroupHeatmap**](https://zhanghao-njmu.github.io/SCP/reference/GroupHeatmap.html)![Example3](README/README-Example-4.jpg) +[**CellDimPlot**](https://zhanghao-njmu.github.io/SCP/reference/CellDimPlot.html)![Example1](man/figures/Example-1.jpg) [**CellStatPlot**](https://zhanghao-njmu.github.io/SCP/reference/CellStatPlot.html)![Example2](man/figures/Example-2.jpg) [**FeatureStatPlot**](https://zhanghao-njmu.github.io/SCP/reference/FeatureStatPlot.html)![Example3](man/figures/Example-3.jpg) [**GroupHeatmap**](https://zhanghao-njmu.github.io/SCP/reference/GroupHeatmap.html)![Example3](man/figures/Example-4.jpg) You can also find more examples in the documentation of the function: [Integration_SCP](https://zhanghao-njmu.github.io/SCP/reference/Integration_SCP.html), [RunKNNMap](https://zhanghao-njmu.github.io/SCP/reference/RunKNNMap.html), [RunMonocle3](https://zhanghao-njmu.github.io/SCP/reference/RunMonocle3.html), [RunPalantir](https://zhanghao-njmu.github.io/SCP/reference/RunPalantir.html), etc. diff --git a/README.md b/README.md index fe1e9dd2..e4b1694c 100644 --- a/README.md +++ b/README.md @@ -66,7 +66,7 @@ if (!require("devtools", quietly = TRUE)) { devtools::install_github("zhanghao-njmu/SCP") ``` -#### Create SCP python environment +#### Create a python environment for SCP To run functions such as `RunPAGA` or `RunSCVELO`, SCP requires [conda](https://docs.conda.io/en/latest/miniconda.html) to create a @@ -253,7 +253,7 @@ CellDimPlot( ) ``` - + ``` r CellDimPlot( @@ -262,7 +262,7 @@ CellDimPlot( ) ``` - + ``` r FeatureDimPlot( @@ -271,7 +271,7 @@ FeatureDimPlot( ) ``` - + ``` r FeatureDimPlot( @@ -281,7 +281,7 @@ FeatureDimPlot( ) ``` - + ``` r ht <- GroupHeatmap( @@ -303,7 +303,7 @@ ht <- GroupHeatmap( print(ht$plot) ``` - + ### CellQC @@ -312,13 +312,13 @@ pancreas_sub <- RunCellQC(srt = pancreas_sub) CellDimPlot(srt = pancreas_sub, group.by = "CellQC", reduction = "UMAP") ``` - + ``` r CellStatPlot(srt = pancreas_sub, stat.by = "CellQC", group.by = "CellType", label = TRUE) ``` - + ``` r CellStatPlot( @@ -331,7 +331,7 @@ CellStatPlot( ) ``` - + ### Standard pipeline @@ -343,19 +343,19 @@ CellDimPlot( ) ``` - + ``` r CellDimPlot3D(srt = pancreas_sub, group.by = "SubCellType") ``` -![CellDimPlot3D](README/README-CellDimPlot3D-1.png) +![CellDimPlot3D](man/figures/CellDimPlot3D-1.png) ``` r FeatureDimPlot3D(srt = pancreas_sub, features = c("Sox9", "Neurog3", "Fev", "Rbp4")) ``` -![FeatureDimPlot3D](README/README-FeatureDimPlot3D-1.png) +![FeatureDimPlot3D](man/figures/FeatureDimPlot3D-1.png) ### Integration pipeline @@ -371,11 +371,11 @@ CellDimPlot( ) ``` - + UMAP embeddings based on different integration methods in SCP: -![Integration-all](README/README-Integration-all.png) +![Integration-all](man/figures/Integration-all.png) ### Cell projection between single-cell datasets @@ -392,7 +392,7 @@ ProjectionPlot( ) ``` - + ### Cell annotation using bulk RNA-seq datasets @@ -402,7 +402,7 @@ pancreas_sub <- RunKNNPredict(srt_query = pancreas_sub, bulk_ref = ref_scMCA, fi CellDimPlot(srt = pancreas_sub, group.by = "KNNPredict_classification", reduction = "UMAP", label = TRUE) ``` - + ### Cell annotation using single-cell datasets @@ -414,7 +414,7 @@ pancreas_sub <- RunKNNPredict( CellDimPlot(srt = pancreas_sub, group.by = "KNNPredict_classification", reduction = "UMAP", label = TRUE) ``` - + ``` r @@ -426,7 +426,7 @@ pancreas_sub <- RunKNNPredict( CellDimPlot(srt = pancreas_sub, group.by = "KNNPredict_classification", reduction = "UMAP", label = TRUE) ``` - + ``` r @@ -439,7 +439,7 @@ ht <- CellCorHeatmap( print(ht$plot) ``` - + ### PAGA analysis @@ -451,7 +451,7 @@ pancreas_sub <- RunPAGA( PAGAPlot(srt = pancreas_sub, reduction = "UMAP", label = TRUE, label_insitu = TRUE, label_repel = TRUE) ``` - + ### Velocity analysis @@ -470,13 +470,13 @@ pancreas_sub <- RunSCVELO( VelocityPlot(srt = pancreas_sub, reduction = "UMAP", group_by = "SubCellType") ``` - + ``` r VelocityPlot(srt = pancreas_sub, reduction = "UMAP", plot_type = "stream") ``` - + ### Differential expression analysis @@ -485,7 +485,7 @@ pancreas_sub <- RunDEtest(srt = pancreas_sub, group_by = "CellType", fc.threshol VolcanoPlot(srt = pancreas_sub, group_by = "CellType") ``` - + ``` r DEGs <- pancreas_sub@tools$DEtest_CellType$AllMarkers_wilcox @@ -501,7 +501,7 @@ ht <- FeatureHeatmap( print(ht$plot) ``` - + ### Enrichment analysis(over-representation) @@ -516,7 +516,7 @@ EnrichmentPlot( ) ``` - + ``` r EnrichmentPlot( @@ -525,7 +525,7 @@ EnrichmentPlot( ) ``` - + ``` r EnrichmentPlot( @@ -534,7 +534,7 @@ EnrichmentPlot( ) ``` - + ``` r EnrichmentPlot( @@ -543,7 +543,7 @@ EnrichmentPlot( ) ``` - + > To ensure that labels are visible, you can adjust the size of the > viewer panel on Rstudio IDE. @@ -555,13 +555,13 @@ EnrichmentPlot( ) ``` - + ``` r EnrichmentPlot(srt = pancreas_sub, group_by = "CellType", plot_type = "comparison") ``` - + ### Enrichment analysis(GSEA) @@ -573,7 +573,7 @@ pancreas_sub <- RunGSEA( GSEAPlot(srt = pancreas_sub, group_by = "CellType", group_use = "Endocrine", id_use = "GO:0007186") ``` - + ``` r GSEAPlot( @@ -582,13 +582,13 @@ GSEAPlot( ) ``` - + ``` r GSEAPlot(srt = pancreas_sub, group_by = "CellType", plot_type = "comparison") ``` - + ### Trajectory inference @@ -596,19 +596,19 @@ GSEAPlot(srt = pancreas_sub, group_by = "CellType", plot_type = "comparison") pancreas_sub <- RunSlingshot(srt = pancreas_sub, group.by = "SubCellType", reduction = "UMAP") ``` - + ``` r FeatureDimPlot(pancreas_sub, features = paste0("Lineage", 1:3), reduction = "UMAP", theme_use = "theme_blank") ``` - + ``` r CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", lineages = paste0("Lineage", 1:3), lineages_span = 0.1) ``` - + ### Dynamic features @@ -627,7 +627,7 @@ ht <- DynamicHeatmap( print(ht$plot) ``` - + ``` r DynamicPlot( @@ -637,7 +637,7 @@ DynamicPlot( ) ``` - + ``` r FeatureStatPlot( @@ -651,7 +651,7 @@ FeatureStatPlot( ) ``` - + ### Interactive data visualization with SCExplorer @@ -665,15 +665,15 @@ if (interactive()) { } ``` -![SCExplorer1](README/README-SCExplorer-1.png) -![SCExplorer2](README/README-SCExplorer-2.png) +![SCExplorer1](man/figures/SCExplorer-1.png) +![SCExplorer2](man/figures/SCExplorer-2.png) ### Other visualization examples -[**CellDimPlot**](https://zhanghao-njmu.github.io/SCP/reference/CellDimPlot.html)![Example1](README/README-Example-1.jpg) -[**CellStatPlot**](https://zhanghao-njmu.github.io/SCP/reference/CellStatPlot.html)![Example2](README/README-Example-2.jpg) -[**FeatureStatPlot**](https://zhanghao-njmu.github.io/SCP/reference/FeatureStatPlot.html)![Example3](README/README-Example-3.jpg) -[**GroupHeatmap**](https://zhanghao-njmu.github.io/SCP/reference/GroupHeatmap.html)![Example3](README/README-Example-4.jpg) +[**CellDimPlot**](https://zhanghao-njmu.github.io/SCP/reference/CellDimPlot.html)![Example1](man/figures/Example-1.jpg) +[**CellStatPlot**](https://zhanghao-njmu.github.io/SCP/reference/CellStatPlot.html)![Example2](man/figures/Example-2.jpg) +[**FeatureStatPlot**](https://zhanghao-njmu.github.io/SCP/reference/FeatureStatPlot.html)![Example3](man/figures/Example-3.jpg) +[**GroupHeatmap**](https://zhanghao-njmu.github.io/SCP/reference/GroupHeatmap.html)![Example3](man/figures/Example-4.jpg) You can also find more examples in the documentation of the function: [Integration_SCP](https://zhanghao-njmu.github.io/SCP/reference/Integration_SCP.html), diff --git a/README/README-CellDimPlot3D-1.png b/man/figures/CellDimPlot3D-1.png similarity index 100% rename from README/README-CellDimPlot3D-1.png rename to man/figures/CellDimPlot3D-1.png diff --git a/README/README-DynamicHeatmap-1.png b/man/figures/DynamicHeatmap-1.png similarity index 100% rename from README/README-DynamicHeatmap-1.png rename to man/figures/DynamicHeatmap-1.png diff --git a/README/README-DynamicPlot-1.png b/man/figures/DynamicPlot-1.png similarity index 100% rename from README/README-DynamicPlot-1.png rename to man/figures/DynamicPlot-1.png diff --git a/README/README-EDA-1.png b/man/figures/EDA-1.png similarity index 100% rename from README/README-EDA-1.png rename to man/figures/EDA-1.png diff --git a/README/README-EDA-2.png b/man/figures/EDA-2.png similarity index 100% rename from README/README-EDA-2.png rename to man/figures/EDA-2.png diff --git a/README/README-EDA-3.png 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