update README

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

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)<!-- -->