<!– badges: end –>

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.

The main benefits are

• in interactive mode you can draw your gates on extensive ggplot-like scatter plots
• you can draw multiple gates
• you can save your gates and apply the programmatically.

Input (tibble)

Command input %>% gate(element, dimension1, dimension2)

Output (tibble)

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

tidygate_gate <-
  tidygate_data %>%
  mutate( gate = gate_chr( Dim1, Dim2 ) )


tidygate_gate

Gates are saved in a temporary file for later use

## [[1]]
##            x          y
## 1 -0.9380459  0.2784375
## 2 -0.9555544 -0.1695209
## 3 -0.3310857  0.2116150
## 
## [[2]]
##             x          y
## 1  0.01324749  0.2165648
## 2 -0.31065917 -0.1026984
## 3 -0.11514794 -0.2982161
## 4  0.48013998  0.1225183

Programmatic gating

We can use previously drawn gates to programmately add the gate column

tidygate_data %>%
  mutate( gate = gate_chr(
    Dim1, Dim2,
     # Pre-defined gates
    gate_list = my_gates
  ))

## # A tibble: 2,240 × 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 endothelial epithe…    -1    ACC       -0.874 -0.239  0    
##  2 adrenal         1 endothelial fibrob…    -1    ACC       -0.740  0.114  1    
##  3 adrenal         1 endothelial immune…    -1    ACC       -0.988  0.118  0    
##  4 adrenal         1 epithelial  endoth…     1    ACC        0.851  0.261  0    
##  5 adrenal         1 epithelial  fibrob…     1    ACC        0.839  0.320  0    
##  6 adrenal         1 epithelial  immune…     1    ACC        0.746  0.337  0    
##  7 adrenal         1 fibroblast  endoth…     1    ACC        0.722 -0.0696 0    
##  8 adrenal         1 fibroblast  epithe…    -1    ACC       -0.849 -0.317  0    
##  9 adrenal         1 fibroblast  immune…     0.52 ACC       -0.776 -0.383  0    
## 10 adrenal         1 immune_cell endoth…     1    ACC        0.980 -0.116  0    
## # … with 2,230 more rows