Description Usage Arguments Value See Also Examples

View source: R/normalization.R

Normalizes an abundance table to the desired number of ranks

1 2 3 | ```
RADnormalization_matrix(input, max_rank, average_over = 1, min_rank = 1,
labels = FALSE, count_data = TRUE, sample_in_row = TRUE,
method = "upperlimit", verbose = T)
``` |

`input` |
A vector or matrix which contains the abundance values (an abundance table). |

`max_rank` |
The desired rank to which this method normalizes the input. |

`average_over` |
Number of times, a normalized RAD is created and averaged to produce the result. |

`min_rank` |
The minimum rank to which this method normalizes the input. |

`labels` |
A logical. If |

`count_data` |
A logical. |

`sample_in_row` |
A logical. |

`method` |
Sets the stop criterion for normalization. This should be one of "lowerlimit", "middle" or "upperlimit". Method affects the final result. lowerlimit: Samples from species pool one by one, until reaches max_rank. middle: Samples from species pool with random size until the sampled vector has desired ranks (max_rank). upperlimit: Removes from species pool one by one, until reaches max_rank. |

`verbose` |
A logical. If |

A list of following items:

$norm_matrix A matrix which contains normalized RADs sum up to 1. If `labels = TRUE`

, it would also contain the labels.

$inputs A list which contains inputs used for creating normalized RADs. It does not contain `input`

because it could be very big.

`RADnormalization`

for normalize an abundance vector. This function return more details compared to `RADnormalization_matrix`

,
`representative_point`

for study the representative of groups of samples in a multi-dimensional scaling plot,
`representative_RAD`

for study the representative of group of norm rads.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | ```
data("gut_otu_table")
rads <- gut_otu_table
#plot original rads
line_cols <- c("green","red","blue")
sample_classes <- c(1,1,1,1,2,2,3,3,1,1,2,3,3,1,1,2,3,3)
plot(1,xlim = c(1,2000),ylim = c(1,20000),col = "white",log = "xy",
xlab = "Rank",ylab = "Abundance",main = "Original RADs from antibiotic data set")
for(i in 1:nrow(rads)){
temp <- sort(rads[i,],decreasing = TRUE)
temp <- temp[temp>0]
lines(x = temp,lwd = 2,col = line_cols[sample_classes[i]])
}
legend("bottomleft",bty = "n",legend = c("pre Cp","under Cp","post Cp"),col = line_cols,lwd = 3)
nrads <- RADnormalization_matrix(input = rads,max_rank = 400,average_over = 20,sample_in_row = TRUE)
nrads <- nrads$norm_matrix
plot(1,xlim = c(1,400),ylim = c(4e-5,1),col = "white",log = "xy",
xlab = "Rank",ylab = "Abundance",
main = "NRADs from antibiotic data set with R = 400 \n with average_over = 20")
for(i in 1:nrow(nrads)){
lines(x = nrads[i,],lwd = 2,col = line_cols[sample_classes[i]])
}
legend("bottomleft",bty = "n",legend = c("pre Cp","under Cp","post Cp"),col = line_cols,lwd = 3)
``` |

```
1 ( 5.56 %) |2 ( 11.11 %) |3 ( 16.67 %) |4 ( 22.22 %) |5 ( 27.78 %) |6 ( 33.33 %) |7 ( 38.89 %) |8 ( 44.44 %) |9 ( 50 %) |10 ( 55.56 %) |11 ( 61.11 %) |12 ( 66.67 %) |13 ( 72.22 %) |14 ( 77.78 %) |15 ( 83.33 %) |16 ( 88.89 %) |17 ( 94.44 %) |18 ( 100 %) |
```

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