Please have a look also to
nanny for tidy high-level data analysis and manipulation
tidyHeatmap for producing heatmaps following tidy principles
tidybulk for tidy and modular transcriptomics analyses
# From Github
devtools::install_github("stemangiola/tidygate")
# From CRAN
install.package("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.
The main benefits are
A tibble of this kind
| dimension1 | dimension2 | annotations |
|-----------------|------------|-------------|
| chr
or fctr
| numeric
| … |
tidygate_gate <-
tidygate_data %>%
mutate( gate = gate_chr( Dim1, Dim2 ) )
escape
on your keyboardtidygate_gate
## # 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
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
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 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
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