diff --git a/README.Rmd b/README.Rmd index 6886246..e67705d 100644 --- a/README.Rmd +++ b/README.Rmd @@ -72,6 +72,27 @@ p + geom_overlay("IgD-CD27-", alpha = 0.5, size = 0.1, color = "purple") fs <- getData(gs, "CD20") #extract the gated data as a flowSet autoplot(fs, "CD20", "CD19") #plot 2D ``` +```{r} +gs1 <- gs[1] +gs2 <- gs[2] +#construct the ggcyto object for gs1 +p <- ggcyto(gs1, aes(cd24, cd38)) + geom_hex(bins = 128) +p <- p + geom_gate("Transitional") #add gate +#customize the stats layer +p <- p + geom_stats(type = "count", size = 6, color = "red", fill = "green", adjust = 0.7) +#customize the layer +p <- p + labs_cyto("channel") +#customize the axis limits +p <- p + ggcyto_par_set(limits = "instrument") +#add another population as the overlay dots +p <- p + geom_overlay("IgD-CD27-", col = "black", size = 1.2, alpha = 0.4) +#hide the legend +p <- p + guides(fill=FALSE) +p + +#replace the data with gs2 and see the same visual effect +p %+% gs2 +``` ```{r fig.height = 1} autoplot(fs, "CD20") #1d density diff --git a/README.md b/README.md index d6de366..549df18 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,14 @@ -# ggcyto : Visualize `Cytometry` data with `ggplot`' - +--- +title: 'ggcyto : Visualize `Cytometry` data with `ggplot`' +output: + html_document: + fig_height: 1 + fig_width: 1 + keep_md: yes +vignette: > + %\VignetteEngine{knitr::rmarkdown} + %\VignetteIndexEntry{Feature summary of ggcyto} +--- `ggcyto` is a cytometry data visualization tool built around ggplot and the grammar of graphics paradigm. The software extends the popular ggplot2 framework, already familiar to many data scientists, enabling it to recog-nize the core Bioconductor flow cytometry data structures for gated and annotated cytometry data. It simplifies visualization and plotting of flow data for publication quality graphics. @@ -93,12 +102,40 @@ autoplot(fs, "CD20", "CD19") #plot 2D ![](README_files/figure-html/unnamed-chunk-4-7.png) +```r +gs1 <- gs[1] +gs2 <- gs[2] +#construct the ggcyto object for gs1 +p <- ggcyto(gs1, aes(cd24, cd38)) + geom_hex(bins = 128) +p <- p + geom_gate("Transitional") #add gate +#customize the stats layer +p <- p + geom_stats(type = "count", size = 6, color = "red", fill = "green", adjust = 0.7) +#customize the layer +p <- p + labs_cyto("channel") +#customize the axis limits +p <- p + ggcyto_par_set(limits = "instrument") +#add another population as the overlay dots +p <- p + geom_overlay("IgD-CD27-", col = "black", size = 1.2, alpha = 0.4) +#hide the legend +p <- p + guides(fill=FALSE) +p +``` + +![](README_files/figure-html/unnamed-chunk-5-1.png) + +```r +#replace the data with gs2 and see the same visual effect +p %+% gs2 +``` + +![](README_files/figure-html/unnamed-chunk-5-2.png) + ```r autoplot(fs, "CD20") #1d density ``` -![](README_files/figure-html/unnamed-chunk-5-1.png) +![](README_files/figure-html/unnamed-chunk-6-1.png) ```r #extract one sample as a flowFrame @@ -107,7 +144,7 @@ fr <- fs[[1]] autoplot(fr) ``` -![](README_files/figure-html/unnamed-chunk-6-1.png) +![](README_files/figure-html/unnamed-chunk-7-1.png) @@ -119,7 +156,7 @@ p <- autoplot(gh, nodes, bins = 64) p ``` -![](README_files/figure-html/unnamed-chunk-7-1.png) +![](README_files/figure-html/unnamed-chunk-8-1.png) ```r @@ -128,7 +165,7 @@ gt <- ggcyto_arrange(p, nrow = 1) plot(gt) ``` -![](README_files/figure-html/unnamed-chunk-8-1.png) +![](README_files/figure-html/unnamed-chunk-9-1.png) diff --git a/README_files/figure-html/unnamed-chunk-4-1.png b/README_files/figure-html/unnamed-chunk-4-1.png index 840ca0a..2241eff 100755 Binary files a/README_files/figure-html/unnamed-chunk-4-1.png and b/README_files/figure-html/unnamed-chunk-4-1.png differ diff --git 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