Merge pull request #5 from stemangiola/make-element-optional

Make element optional

README.Rmd

@@ -20,6 +20,9 @@ library(knitr)
 knitr::opts_chunk$set(cache = TRUE, warning = FALSE,
                       message = FALSE, cache.lazy = FALSE)
 
+library(dplyr)
+library(tidygate)
+
 ```
 
 It interactively or programmately labels points within custom gates on two dimensions, according to tidyverse principles. The information is added to your tibble. It is based on the package `gatepoints` from Wajid Jawaid. 
@@ -58,3 +61,58 @@ devtools::install_github("stemangiola/tidygate")
 
 ```
 
+## Interactive gating
+
+The standard way to gate points in a two-dimensional plot is to 
+- Interactively draw an arbitrary number of gates
+- Click "Finish" button on the top-right corner of the plot
+
+```{r, eval = FALSE}
+tidygate_gate <-
+  tidygate_data %>%
+  gate( 
+    
+    # grouping by
+    c(`ct 1`, `ct 2`), 
+    
+    # Dimensions
+    Dim1, Dim2
+  )
+
+tidygate_gate
+```
+
+We can save our gates in a separate variable for later use
+
+```{r, eval = FALSE}
+my_gates = tidygate_gate %>% attr("gate")
+
+my_gates
+```
+
+```{r, echo = FALSE}
+my_gates = tidygate::gate_list
+```
+
+## Programmatic gating
+
+We can use previously drawn gates to programmately add the gate column 
+
+```{r}
+
+tidygate_data %>%
+  gate( 
+    
+    # grouping by
+    c(`ct 1`, `ct 2`), 
+    
+    # Dimensions
+    Dim1, Dim2,
+    
+    # Pre-defined gates
+    gate_list = my_gates
+  )
+
+```
+
+

README.md

@@ -2,16 +2,22 @@ tidygate: add gate information to your tibble
 ================
 
 <!---
-
 [![Build Status](https://travis-ci.org/stemangiola/tidygate.svg?branch=master)](https://travis-ci.org/stemangiola/tidygate) [![Coverage Status](https://coveralls.io/repos/github/stemangiola/tidygate/badge.svg?branch=master)](https://coveralls.io/github/stemangiola/tidygate?branch=master)
-
 -->
 
 <!-- badges: start -->
 
 [![Lifecycle:maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
 <!-- badges: end -->
 
+Please have a look also to -
+[nanny](https://github.com/stemangiola/nanny) for tidy high-level data
+analysis and manipulation -
+[tidyHeatmap](https://github.com/stemangiola/tidyHeatmap) for producing
+heatmaps following tidy principles -
+[tidybulk](https://github.com/stemangiola/tidybulk) for tidy and modular
+transcriptomics analyses
+
 It interactively or programmately labels points within custom gates on
 two dimensions, according to tidyverse principles. The information is
 added to your tibble. It is based on the package `gatepoints` from Wajid
@@ -45,3 +51,66 @@ The main benefits are
 ``` r
 devtools::install_github("stemangiola/tidygate")
 ```
+
+## Interactive gating
+
+The standard way to gate points in a two-dimensional plot is to -
+Interactively draw an arbitrary number of gates - Click “Finish” button
+on the top-right corner of the plot
+
+``` r
+tidygate_gate <-
+  tidygate_data %>%
+  gate( 
+
+    # grouping by
+    c(`ct 1`, `ct 2`), 
+
+    # Dimensions
+    Dim1, Dim2
+  )
+
+tidygate_gate
+```
+
+We can save our gates in a separate variable for later use
+
+``` r
+my_gates = tidygate_gate %>% attr("gate")
+
+my_gates
+```
+
+## Programmatic gating
+
+We can use previously drawn gates to programmately add the gate column
+
+``` r
+tidygate_data %>%
+  gate( 
+
+    # grouping by
+    c(`ct 1`, `ct 2`), 
+
+    # Dimensions
+    Dim1, Dim2,
+
+    # Pre-defined gates
+    gate_list = my_gates
+  )
+```
+
+    ## # A tibble: 2,240 x 9
+    ##    group   hierarchy `ct 1`    `ct 2`    relation cancer_ID   Dim1    Dim2 gate 
+    ##    <chr>       <dbl> <chr>     <chr>        <dbl> <chr>      <dbl>   <dbl> <chr>
+    ##  1 adrenal         1 endothel… epitheli…    -1    ACC       -0.874 -0.239  0    
+    ##  2 adrenal         1 endothel… fibrobla…    -1    ACC       -0.740  0.114  1    
+    ##  3 adrenal         1 endothel… immune_c…    -1    ACC       -0.988  0.118  0    
+    ##  4 adrenal         1 epitheli… endothel…     1    ACC        0.851  0.261  0    
+    ##  5 adrenal         1 epitheli… fibrobla…     1    ACC        0.839  0.320  0    
+    ##  6 adrenal         1 epitheli… immune_c…     1    ACC        0.746  0.337  0    
+    ##  7 adrenal         1 fibrobla… endothel…     1    ACC        0.722 -0.0696 0    
+    ##  8 adrenal         1 fibrobla… epitheli…    -1    ACC       -0.849 -0.317  0    
+    ##  9 adrenal         1 fibrobla… immune_c…     0.52 ACC       -0.776 -0.383  0    
+    ## 10 adrenal         1 immune_c… endothel…     1    ACC        0.980 -0.116  0    
+    ## # … with 2,230 more rows

vignettes/introdution.Rmd

@@ -26,7 +26,8 @@ library(knitr)
 knitr::opts_chunk$set(cache = TRUE, warning = FALSE,
                       message = FALSE, cache.lazy = FALSE)
 
-
+library(dplyr)
+library(tidygate)
 
 ```
 
@@ -58,6 +59,56 @@ element |  dimension1 | dimension2 | annotations | Gate |
 `chr` or `fctr` | `chr` or `fctr` | `numeric` | ... | ...
 
 
+## Interactive gating
+
+The standard way to gate points in a two-dimensional plot is to 
+- Interactively draw an arbitrary number of gates
+- Click "Finish" button on the top-right corner of the plot
+
+```{r, eval = FALSE}
+tidygate_gate <-
+  tidygate_data %>%
+  gate( 
+    
+    # grouping by
+    c(`ct 1`, `ct 2`), 
+    
+    # Dimensions
+    Dim1, Dim2
+  )
+
+tidygate_gate
+```
+
+We can save our gates in a separate variable for later use
+
+```{r, eval = FALSE}
+my_gates = tidygate_gate %>% attr("gate")
+
+my_gates
+```
+
+```{r, echo = FALSE}
+my_gates = tidygate::gate_list
+```
+
+## Programmatic gating
+
+We can use previously drawn gates to programmately add the gate column 
 
+```{r}
 
+tidygate_data %>%
+  gate( 
+    
+    # grouping by
+    c(`ct 1`, `ct 2`), 
+    
+    # Dimensions
+    Dim1, Dim2,
+    
+    # Pre-defined gates
+    gate_list = my_gates
+  )
 
+```