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update README
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mikejiang committed Apr 3, 2018
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21 changes: 21 additions & 0 deletions README.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
49 changes: 43 additions & 6 deletions README.md
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@@ -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.
Expand Down Expand Up @@ -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
Expand All @@ -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)<!-- -->



Expand All @@ -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
Expand All @@ -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)<!-- -->



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