Convert contrast to short-form comp, convert comp to contrast (DEV)
Source:R/jam_contrast2comp_dev.R
contrast2comp_dev.RdConvert contrast to short-form comp, convert comp to contrast (DEV)
Details
This method is developmental and is being tested as potentially
faster version of contrast2comp().
See also
Other jamses utilities:
choose_annotation_colnames(),
fold_to_log2fold(),
intercalate(),
list2im_opt(),
log2fold_to_fold(),
make_block_arrow_polygon(),
mark_stat_hits(),
matrix_normalize(),
point_handedness(),
point_slope_intercept(),
shortest_unique_abbreviation(),
shrinkDataFrame(),
shrink_df(),
shrink_matrix(),
sort_samples(),
strsplitOrdered(),
sub_split_vector(),
update_function_params(),
update_list_elements()
Examples
contrast_names1 <- c("(A_c-B_c)-(A_d-B_d)",
"A_c-B_c",
"GroupA-GroupB",
"((A_c_J-B_c_J)-(A_d_J-B_d_J))-((A_c_W-B_c_W)-(A_d_W-B_d_W))")
contrast2comp_dev(contrast_names1)
#> [1] "A-B:c-d" "A-B:c" "GroupA-GroupB" "A-B:c-d:J-W"
# Note: this function fails when contrasts are not balanced
contrast2comp_dev(c("(A_c-B_c)-(A_d-C_d)"), verbose=TRUE)
#> ## (14:55:35) 28Oct2024: contrast2comp_dev(): ilist:
#> $`(A_c-B_c)-(A_d-C_d)`
#> [1] "" "A_c" "B_c" "A_d" "C_d"
#>
#> ## (14:55:35) 28Oct2024: contrast2comp_dev(): idf:
#> C B A.1 A.2 split1
#> (A_c-B_c)-(A_d-C_d)2 (A_c-B_c)-(A_d-C_d) (A_c-B_c)-(A_d-C_d) A c 1
#> (A_c-B_c)-(A_d-C_d)3 (A_c-B_c)-(A_d-C_d) (A_c-B_c)-(A_d-C_d) B c 1
#> (A_c-B_c)-(A_d-C_d)4 (A_c-B_c)-(A_d-C_d) (A_c-B_c)-(A_d-C_d) A d 2
#> (A_c-B_c)-(A_d-C_d)5 (A_c-B_c)-(A_d-C_d) (A_c-B_c)-(A_d-C_d) C d 2
#> idf_B_split
#> (A_c-B_c)-(A_d-C_d)2 A
#> (A_c-B_c)-(A_d-C_d)3 A
#> (A_c-B_c)-(A_d-C_d)4 B
#> (A_c-B_c)-(A_d-C_d)5 B
#> ## (14:55:35) 28Oct2024: contrast2comp_dev(): idf_new:
#> C B A.1 A.2 split2
#> A (A_c-B_c)-(A_d-C_d) (A_c-B_c)-(A_d-C_d) A-B c 1
#> B (A_c-B_c)-(A_d-C_d) (A_c-B_c)-(A_d-C_d) A-C d 1
#> ## (14:55:35) 28Oct2024: contrast2comp_dev(): idf_newer:
#> C B A.1 A.2
#> (A_c-B_c)-(A_d-C_d) (A_c-B_c)-(A_d-C_d) (A_c-B_c)-(A_d-C_d) A-B-A-C c-d
#> ## (14:55:35) 28Oct2024: contrast2comp_dev(): two-way imbalance:
#> A.1 A.2
#> TRUE FALSE
#> ## (14:55:36) 28Oct2024: contrast2comp_dev(): idf_newer:
#> C B A.1 A.2 newB
#> (A_c-B_c)-(A_d-C_d)_v1 v1 (A_c-B_c)-(A_d-C_d)_v1 A-B c (A_c-B_c)-(A_d-C_d)
#> (A_c-B_c)-(A_d-C_d)_v2 v2 (A_c-B_c)-(A_d-C_d)_v2 A-C d (A_c-B_c)-(A_d-C_d)
#> ## (14:55:36) 28Oct2024: contrast2comp_dev(): idf_newer:
#> C B A.1 A.2 newB
#> (A_c-B_c)-(A_d-C_d)_v1 v1 (A_c-B_c)-(A_d-C_d)_v1 A-B c (A_c-B_c)-(A_d-C_d)
#> (A_c-B_c)-(A_d-C_d)_v2 v2 (A_c-B_c)-(A_d-C_d)_v2 A-C d (A_c-B_c)-(A_d-C_d)
#> comp
#> (A_c-B_c)-(A_d-C_d)_v1 A-B:c
#> (A_c-B_c)-(A_d-C_d)_v2 A-C:d
#> [1] "(A-B:c)-(A-C:d)"
contrast2comp(c("(A_c-B_c)-(A_d-C_d)"), verbose=TRUE)
#> ## (14:55:36) 28Oct2024: im:
#> [,1] [,2]
#> [1,] "A" "c"
#> [2,] "B" "c"
#> [3,] "A" "d"
#> [4,] "C" "d"
#> ## (14:55:36) 28Oct2024: imnew:
#> [,1] [,2]
#> [1,] "A-B" "c"
#> [2,] "A-C" "d"
#> [1] "(A-B:c)-(A-C:d)"
contrast2comp_dev(c(contrast_names1[1:2], "(A_c-B_c)-(A_d-C_d)"), verbose=TRUE)
#> ## (14:55:36) 28Oct2024: contrast2comp_dev(): ilist:
#> $`(A_c-B_c)-(A_d-B_d)`
#> [1] "" "A_c" "B_c" "A_d" "B_d"
#>
#> $`A_c-B_c`
#> [1] "A_c" "B_c"
#>
#> $`(A_c-B_c)-(A_d-C_d)`
#> [1] "" "A_c" "B_c" "A_d" "C_d"
#>
#> ## (14:55:36) 28Oct2024: contrast2comp_dev(): idf:
#> C B A.1 A.2 split1
#> (A_c-B_c)-(A_d-B_d)2 (A_c-B_c)-(A_d-B_d) (A_c-B_c)-(A_d-B_d) A c 1
#> (A_c-B_c)-(A_d-B_d)3 (A_c-B_c)-(A_d-B_d) (A_c-B_c)-(A_d-B_d) B c 1
#> (A_c-B_c)-(A_d-B_d)4 (A_c-B_c)-(A_d-B_d) (A_c-B_c)-(A_d-B_d) A d 2
#> (A_c-B_c)-(A_d-B_d)5 (A_c-B_c)-(A_d-B_d) (A_c-B_c)-(A_d-B_d) B d 2
#> A_c-B_c1 A_c-B_c A_c-B_c A c 3
#> A_c-B_c2 A_c-B_c A_c-B_c B c 3
#> (A_c-B_c)-(A_d-C_d)2 (A_c-B_c)-(A_d-C_d) (A_c-B_c)-(A_d-C_d) A c 4
#> (A_c-B_c)-(A_d-C_d)3 (A_c-B_c)-(A_d-C_d) (A_c-B_c)-(A_d-C_d) B c 4
#> (A_c-B_c)-(A_d-C_d)4 (A_c-B_c)-(A_d-C_d) (A_c-B_c)-(A_d-C_d) A d 5
#> (A_c-B_c)-(A_d-C_d)5 (A_c-B_c)-(A_d-C_d) (A_c-B_c)-(A_d-C_d) C d 5
#> idf_B_split
#> (A_c-B_c)-(A_d-B_d)2 A
#> (A_c-B_c)-(A_d-B_d)3 A
#> (A_c-B_c)-(A_d-B_d)4 B
#> (A_c-B_c)-(A_d-B_d)5 B
#> A_c-B_c1 C
#> A_c-B_c2 C
#> (A_c-B_c)-(A_d-C_d)2 D
#> (A_c-B_c)-(A_d-C_d)3 D
#> (A_c-B_c)-(A_d-C_d)4 E
#> (A_c-B_c)-(A_d-C_d)5 E
#> ## (14:55:36) 28Oct2024: contrast2comp_dev(): idf_new:
#> C B A.1 A.2 split2
#> A (A_c-B_c)-(A_d-B_d) (A_c-B_c)-(A_d-B_d) A-B c 1
#> B (A_c-B_c)-(A_d-B_d) (A_c-B_c)-(A_d-B_d) A-B d 1
#> C A_c-B_c A_c-B_c A-B c 2
#> D (A_c-B_c)-(A_d-C_d) (A_c-B_c)-(A_d-C_d) A-B c 3
#> E (A_c-B_c)-(A_d-C_d) (A_c-B_c)-(A_d-C_d) A-C d 3
#> ## (14:55:36) 28Oct2024: contrast2comp_dev(): idf_newer:
#> C B A.1 A.2
#> (A_c-B_c)-(A_d-B_d) (A_c-B_c)-(A_d-B_d) (A_c-B_c)-(A_d-B_d) A-B c-d
#> A_c-B_c A_c-B_c A_c-B_c A-B c
#> (A_c-B_c)-(A_d-C_d) (A_c-B_c)-(A_d-C_d) (A_c-B_c)-(A_d-C_d) A-B-A-C c-d
#> ## (14:55:36) 28Oct2024: contrast2comp_dev(): two-way imbalance:
#> A.1 A.2
#> [1,] FALSE FALSE
#> [2,] FALSE FALSE
#> [3,] TRUE FALSE
#> ## (14:55:36) 28Oct2024: contrast2comp_dev(): idf_newer:
#> C B A.1 A.2 newB
#> (A_c-B_c)-(A_d-B_d) (A_c-B_c)-(A_d-B_d) A-B c-d (A_c-B_c)-(A_d-B_d)
#> A_c-B_c A_c-B_c A-B c A_c-B_c
#> (A_c-B_c)-(A_d-C_d)_v1 v1 (A_c-B_c)-(A_d-C_d)_v1 A-B c (A_c-B_c)-(A_d-C_d)
#> (A_c-B_c)-(A_d-C_d)_v2 v2 (A_c-B_c)-(A_d-C_d)_v2 A-C d (A_c-B_c)-(A_d-C_d)
#> ## (14:55:36) 28Oct2024: contrast2comp_dev(): idf_newer:
#> C B A.1 A.2 newB
#> (A_c-B_c)-(A_d-B_d) (A_c-B_c)-(A_d-B_d) A-B c-d (A_c-B_c)-(A_d-B_d)
#> A_c-B_c A_c-B_c A-B c A_c-B_c
#> (A_c-B_c)-(A_d-C_d)_v1 v1 (A_c-B_c)-(A_d-C_d)_v1 A-B c (A_c-B_c)-(A_d-C_d)
#> (A_c-B_c)-(A_d-C_d)_v2 v2 (A_c-B_c)-(A_d-C_d)_v2 A-C d (A_c-B_c)-(A_d-C_d)
#> comp
#> (A_c-B_c)-(A_d-B_d) A-B:c-d
#> A_c-B_c A-B:c
#> (A_c-B_c)-(A_d-C_d)_v1 A-B:c
#> (A_c-B_c)-(A_d-C_d)_v2 A-C:d
#> [1] "A-B:c-d" "A-B:c" "(A-B:c)-(A-C:d)"