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- < a data-toggle ="collapse " data-parent ="#workflowr-checks " href ="#strongRepositoryversionstrongahrefhttpsgithubcomstephenslabsinglecelljamboreetree82e82de95caf2a23e3550cdd7176a41db356fb48targetblank82e82dea ">
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+ < a data-toggle ="collapse " data-parent ="#workflowr-checks " href ="#strongRepositoryversionstrongahrefhttpsgithubcomstephenslabsinglecelljamboreetree4f94bdf58099ac1226fb66d920018d1da69bb90ctargetblank4f94bdfa ">
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< span class ="glyphicon glyphicon-ok text-success "
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aria-hidden ="true "> </ span > < strong > Repository version:</ strong >
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- < a href ="https://github.com/stephenslab/single-cell-jamboree/tree/82e82de95caf2a23e3550cdd7176a41db356fb48 " target ="_blank "> 82e82de </ a >
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+ < a href ="https://github.com/stephenslab/single-cell-jamboree/tree/4f94bdf58099ac1226fb66d920018d1da69bb90c " target ="_blank "> 4f94bdf </ a >
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- id ="strongRepositoryversionstrongahrefhttpsgithubcomstephenslabsinglecelljamboreetree82e82de95caf2a23e3550cdd7176a41db356fb48targetblank82e82dea "
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+ id ="strongRepositoryversionstrongahrefhttpsgithubcomstephenslabsinglecelljamboreetree4f94bdf58099ac1226fb66d920018d1da69bb90ctargetblank4f94bdfa "
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class ="panel-collapse collapse ">
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< p >
@@ -453,7 +453,7 @@ <h4 class="date">2024-11-15</h4>
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</ p >
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< p >
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The results in this page were generated with repository version
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- < a href ="https://github.com/stephenslab/single-cell-jamboree/tree/82e82de95caf2a23e3550cdd7176a41db356fb48 " target ="_blank "> 82e82de </ a > .
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+ < a href ="https://github.com/stephenslab/single-cell-jamboree/tree/4f94bdf58099ac1226fb66d920018d1da69bb90c " target ="_blank "> 4f94bdf </ a > .
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See the < em > Past versions</ em > tab to see a history of the changes made
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to the R Markdown and HTML files.
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</ p >
@@ -470,7 +470,6 @@ <h4 class="date">2024-11-15</h4>
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Ignored files:
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Ignored: .Rhistory
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@@ -529,6 +528,40 @@ <h4 class="date">2024-11-15</h4>
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Rmd
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+ < a href ="https://github.com/stephenslab/single-cell-jamboree/blob/4f94bdf58099ac1226fb66d920018d1da69bb90c/analysis/mouse_embryo.Rmd " target ="_blank "> 4f94bdf</ a >
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+ Ziang Zhang
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+ 2025-01-22
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+ workflowr::wflow_publish("analysis/mouse_embryo.Rmd")
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+ html
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+ 2025-01-22
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+ Build site.
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< a href ="https://github.com/stephenslab/single-cell-jamboree/blob/82e82de95caf2a23e3550cdd7176a41db356fb48/analysis/mouse_embryo.Rmd " target ="_blank "> 82e82de</ a >
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< td >
@@ -1724,12 +1757,86 @@ <h2>Exploring Spatial Pattern of Factors</h2>
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geom_point(size = 1, alpha = 1) +
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theme_minimal()</ code > </ pre >
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< p > < img src ="figure/mouse_embryo.Rmd/plotting_slide14-1.png " width ="672 " style ="display: block; margin: auto; " /> </ p >
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+ < a href ="https://github.com/stephenslab/single-cell-jamboree/blob/9e347ddd2ead134aeee99a6a393b5f90e0a3c59b/docs/figure/mouse_embryo.Rmd/plotting_slide14-1.png " target ="_blank "> 9e347dd</ a >
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< pre class ="r "> < code > locationsdf %>%
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filter(slideID == "Slide 14") %>%
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ggplot(aes(x = x, y = y, colour = (celltype))) +
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geom_point(size = 1, alpha = 1) +
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theme_minimal()</ code > </ pre >
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< p > < img src ="figure/mouse_embryo.Rmd/plotting_slide14-2.png " width ="672 " style ="display: block; margin: auto; " /> </ p >
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+ < button type ="button " class ="btn btn-default btn-xs btn-workflowr btn-workflowr-fig " data-toggle ="collapse " data-target ="#fig-plotting_slide14-2 ">
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+ < a href ="https://github.com/stephenslab/single-cell-jamboree/blob/9e347ddd2ead134aeee99a6a393b5f90e0a3c59b/docs/figure/mouse_embryo.Rmd/plotting_slide14-2.png " target ="_blank "> 9e347dd</ a >
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< pre class ="r "> < code > plots <- list()
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slideID <- seurat_object$slide_id == "Slide 14"
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selected_factors <- which(order(flashier_fit_nn$pve, decreasing = T) %in% c(1:9))
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# Display the combined plot
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print(combined_plot)</ code > </ pre >
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< p > < img src ="figure/mouse_embryo.Rmd/plotting_slide14_factors-1.png " width ="672 " style ="display: block; margin: auto; " /> </ p >
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+ < button type ="button " class ="btn btn-default btn-xs btn-workflowr btn-workflowr-fig " data-toggle ="collapse " data-target ="#fig-plotting_slide14_factors-1 ">
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+ < a href ="https://github.com/stephenslab/single-cell-jamboree/blob/9e347ddd2ead134aeee99a6a393b5f90e0a3c59b/docs/figure/mouse_embryo.Rmd/plotting_slide14_factors-1.png " target ="_blank "> 9e347dd</ a >
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< pre class ="r "> < code > L <- flashier_fit_semi$L_pm
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slideID <- seurat_object$slide_id == "Slide 14"
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selected_factors <- which(order(flashier_fit_semi$pve, decreasing = T) %in% c(1:9))
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# Display the combined plot
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print(combined_plot)</ code > </ pre >
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< p > < img src ="figure/mouse_embryo.Rmd/plotting_slide14_factors_semi-1.png " width ="672 " style ="display: block; margin: auto; " /> </ p >
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- < pre class ="r "> < code > plots <- list()
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- slideID <- seurat_object$slide_id == "Slide 14"
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- selected_factors <- which(order(flashier_fit_nn$pve, decreasing = T) %in% c(1:9))
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-
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- for (f in selected_factors) {
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- p <- plot_loadings_on_locations(locations = locations, loading = L, factor_num = f, size = 1, which_to_plot = slideID)
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- plots[[length(plots) + 1]] <- ggplotGrob(p)
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- }
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- # Combine the plots in a 2x3 grid
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- combined_plot <- wrap_plots(plots, ncol = 3, nrow = 3)
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-
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- # Display the combined plot
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- print(combined_plot)</ code > </ pre >
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+ < a href ="https://github.com/stephenslab/single-cell-jamboree/blob/9e347ddd2ead134aeee99a6a393b5f90e0a3c59b/docs/figure/mouse_embryo.Rmd/plotting_slide14_factors_semi-1.png " target ="_blank "> 9e347dd</ a >
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< pre class ="r "> < code > # fasttopics_fit <- readRDS("../output/mouse_embryo/fasttopics_fit.rds")
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L <- fasttopics_fit$L
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slideID <- seurat_object$slide_id == "Slide 14"
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# Display the combined plot
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print(combined_plot)</ code > </ pre >
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< p > < img src ="figure/mouse_embryo.Rmd/unnamed-chunk-24-1.png " width ="672 " style ="display: block; margin: auto; " /> </ p >
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< button type ="button " class ="btn btn-default btn-workflowr btn-workflowr-sessioninfo " data-toggle ="collapse " data-target ="#workflowr-sessioninfo " style ="display: block; ">
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