sim_collate | R Documentation |
sim_collate
collates several subsets of a melted similarity matrix,
required for computing metrics.
sim_collate(
sim_df,
all_same_cols_rep,
annotation_cols,
any_different_cols_rep = NULL,
all_different_cols_rep = NULL,
all_same_cols_ref = NULL,
all_same_cols_rep_ref = NULL,
all_same_cols_non_rep = NULL,
any_different_cols_non_rep = NULL,
all_different_cols_non_rep = NULL,
any_different_cols_group = NULL,
all_same_cols_group = NULL,
reference = NULL,
drop_reference = FALSE,
drop_group = NULL
)
sim_df |
|
all_same_cols_rep |
optional character vector specifying columns. |
annotation_cols |
character vector specifying which columns from
|
any_different_cols_rep |
optional character vector specifying columns. |
all_different_cols_rep |
optional character vector specifying columns. |
all_same_cols_ref |
optional character vector specifying columns. |
all_same_cols_rep_ref |
optional character vector specifying columns. |
all_same_cols_non_rep |
optional character vector specifying columns. |
any_different_cols_non_rep |
optional character vector specifying columns. |
all_different_cols_non_rep |
optional character vector specifying columns. |
any_different_cols_group |
optional character vector specifying columns. |
all_same_cols_group |
optional character vector specifying columns. |
reference |
optional character string specifying reference. |
drop_reference |
optional boolean specifying whether to filter (drop)
pairs using |
drop_group |
optional tbl; rows that match on |
Filter out pairs that match drop_group
in either right or left indices
Fetch similarities between
(a) all rows (except, optionally those containing reference
), and
(b) all rows containing reference
Do so only for those (a, b) pairs that
have same values in all columns of all_same_cols_ref
Fetch similarities between
(a) all rows except reference
rows, and
(b) all rows except reference
rows (i.e. to each other)
Do so for only those (a, b) pairs that
have same values in all columns of all_same_cols_rep
have different values in all columns of all_different_cols_rep
(if specified)
have different values in at least one column of
any_different_cols_rep
(if specified)
Keep, both, (a, b) and (b, a)
Fetch similarities between
(a) all rows containing reference
, and
(b) all rows containing reference
(i.e. to each other)
Do so for only those (a, b) pairs that
have same values in all columns of all_same_cols_rep_ref
.
Keep, both, (a, b) and (b, a)
Fetch similarities between
(a) all rows (except, optionally, reference
rows), and
(b) all rows except reference
rows
Do so for only those (a, b) pairs that
have same values in all columns of all_same_cols_non_rep
have different values in all columns all_different_cols_non_rep
have different values in at least one column of
any_different_cols_non_rep
Keep, both, (a, b) and (b, a)
Fetch similarities between
(a) all rows (except, optionally, reference
rows), and
(b) all rows (except, optionally, reference
rows)
Do so for only those (a, b) pairs that
have same values in all columns of all_same_cols_group
have different values in at least one column of
any_different_cols_group
Keep, both, (a, b) and (b, a)
metric_sim
object comprising a filtered sim_df
with
sets of pairs, preserving the same metric_sim
attributes as
sim_df
.
sim_df <- matric::sim_calculate(matric::cellhealth)
drop_group <-
data.frame(Metadata_gene_name = "EMPTY")
reference <-
data.frame(Metadata_gene_name = c("Chr2"))
all_same_cols_ref <-
c(
"Metadata_cell_line",
"Metadata_Plate"
)
all_same_cols_rep <-
c(
"Metadata_cell_line",
"Metadata_gene_name",
"Metadata_pert_name"
)
all_same_cols_rep_ref <-
c(
"Metadata_cell_line",
"Metadata_gene_name",
"Metadata_pert_name",
"Metadata_Plate"
)
any_different_cols_non_rep <-
c(
"Metadata_cell_line",
"Metadata_gene_name",
"Metadata_pert_name"
)
all_same_cols_non_rep <-
c(
"Metadata_cell_line",
"Metadata_Plate"
)
all_different_cols_non_rep <-
c("Metadata_gene_name")
all_same_cols_group <-
c(
"Metadata_cell_line",
"Metadata_gene_name"
)
any_different_cols_group <-
c(
"Metadata_cell_line",
"Metadata_gene_name",
"Metadata_pert_name"
)
annotation_cols <-
c(
"Metadata_cell_line",
"Metadata_gene_name",
"Metadata_pert_name"
)
collated_sim <-
matric::sim_collate(
sim_df,
reference = reference,
all_same_cols_rep = all_same_cols_rep,
all_same_cols_rep_ref = all_same_cols_rep_ref,
all_same_cols_ref = all_same_cols_ref,
any_different_cols_non_rep = any_different_cols_non_rep,
all_same_cols_non_rep = all_same_cols_non_rep,
all_different_cols_non_rep = all_different_cols_non_rep,
any_different_cols_group = any_different_cols_group,
all_same_cols_group = all_same_cols_group,
annotation_cols = annotation_cols,
drop_group = drop_group
)
head(collated_sim)
collated_sim %>%
dplyr::group_by(type) %>%
dplyr::tally()
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