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Sort contrasts by factor and level

Source: R/jam_sort_contrasts.R
sort_contrasts.Rd

Sort contrasts by factor and level, given contrast names, or SEDesign, or data.frame of factors.

Usage

sort_contrasts(x, factor_order = NULL, ...)

Arguments

x

one of:

  • character vector of contrast names

  • SEDesign

  • data.frame with factors

factor_order

integer, default NULL uses all factors, or specify the factor ordering to use for sorting.

...

additional arguments are passed to internal functions. For example 'factor_names' is passed to contrasts_to_factors().

Value

data.frame with factors in each column, and factor levels or factor level contrasts as column values. The rownames() contain contrast names.

Sort order

  • Contrasts are sorted by depth: one-factor comparisons, two-factor comparisons, etc.

  • Contrasts are sorted for factor level contrasts in each factor in factor_order. If factor_order=1 then contrasts appear first in the first factor column.

  • Contrasts are then sorted by that factor column using the observed contrast order.

  • Contrasts are then sorted by other factor columns as they appear in factor_order, using the observed level order in each factor column.

Sort order, described another way:

  • All one-way contrasts will appear at the top.

    • The first one-way contrasts will be comparisons using the first value in factor_order, sorted by the comparison, then sorted by each remaining column in factor_order.

    • The next set of one-way contrasts will be the second value in factor_order, sorted by that comparison, then sorted by each remaining column in factor_order.

  • All two-way contrasts will appear at the end, since each two-way contrast involves two factors.

    • They will be sorted to involve contrasts in the same order as as factor_order.

    • The first two-way contrasts will involve comparisons involving the first two values in factor_order.

See also

Other jam experiment design: SEDesign(), [,SEDesign-method, check_sedesign(), contrast2comp(), contrast_colors_by_group(), contrast_names_to_sedesign(), contrastnames(), contrasts(), contrasts<-(), contrasts_to_factors(), contrasts_to_venn_setlists(), design,SEDesign-method, draw_oneway_contrast(), draw_twoway_contrast(), factors(), filter_contrast_names(), groups(), groups_to_sedesign(), plot.SEDesign(), plot_sedesign(), print,SEDesign-method, samples(), sedesign_to_factors(), validate_sedesign()

Examples

isamples_1 <- paste0(
   rep(c("DMSO", "Etop", "DMSO", "Etop"), each=6),
   "_",
   rep(c("NF", "Flag"), each=12),
   "_",
   rep(c("WT", "KO", "WT", "KO", "WT", "D955N", "WT", "D955N"), each=3),
   "_",
   LETTERS[1:3])
# simple data.frame with group information
idf <- data.frame(jamba::rbindList(strsplit(isamples_1, "_")))[,1:3]
rownames(idf) <- isamples_1;
colnames(idf) <- c("Treatment", "Flag", "Genotype")
# convert to sedesign
sedesign <- groups_to_sedesign(idf)
sort_contrasts(sedesign)
#>                                                               Treatment    Flag
#> Etop_NF_WT-DMSO_NF_WT                                         Etop-DMSO      NF
#> Etop_NF_KO-DMSO_NF_KO                                         Etop-DMSO      NF
#> Etop_Flag_WT-DMSO_Flag_WT                                     Etop-DMSO    Flag
#> Etop_Flag_D955N-DMSO_Flag_D955N                               Etop-DMSO    Flag
#> DMSO_Flag_WT-DMSO_NF_WT                                            DMSO Flag-NF
#> Etop_Flag_WT-Etop_NF_WT                                            Etop Flag-NF
#> DMSO_NF_KO-DMSO_NF_WT                                              DMSO      NF
#> Etop_NF_KO-Etop_NF_WT                                              Etop      NF
#> DMSO_Flag_D955N-DMSO_Flag_WT                                       DMSO    Flag
#> Etop_Flag_D955N-Etop_Flag_WT                                       Etop    Flag
#> (Etop_Flag_WT-DMSO_Flag_WT)-(Etop_NF_WT-DMSO_NF_WT)           Etop-DMSO Flag-NF
#> (Etop_NF_KO-DMSO_NF_KO)-(Etop_NF_WT-DMSO_NF_WT)               Etop-DMSO      NF
#> (Etop_Flag_D955N-DMSO_Flag_D955N)-(Etop_Flag_WT-DMSO_Flag_WT) Etop-DMSO    Flag
#>                                                               Genotype
#> Etop_NF_WT-DMSO_NF_WT                                               WT
#> Etop_NF_KO-DMSO_NF_KO                                               KO
#> Etop_Flag_WT-DMSO_Flag_WT                                           WT
#> Etop_Flag_D955N-DMSO_Flag_D955N                                  D955N
#> DMSO_Flag_WT-DMSO_NF_WT                                             WT
#> Etop_Flag_WT-Etop_NF_WT                                             WT
#> DMSO_NF_KO-DMSO_NF_WT                                            KO-WT
#> Etop_NF_KO-Etop_NF_WT                                            KO-WT
#> DMSO_Flag_D955N-DMSO_Flag_WT                                  D955N-WT
#> Etop_Flag_D955N-Etop_Flag_WT                                  D955N-WT
#> (Etop_Flag_WT-DMSO_Flag_WT)-(Etop_NF_WT-DMSO_NF_WT)                 WT
#> (Etop_NF_KO-DMSO_NF_KO)-(Etop_NF_WT-DMSO_NF_WT)                  KO-WT
#> (Etop_Flag_D955N-DMSO_Flag_D955N)-(Etop_Flag_WT-DMSO_Flag_WT) D955N-WT