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fixes #293

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Sep 8, 2023
Merged

fixes #293

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53 changes: 30 additions & 23 deletions R/functions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -693,7 +693,7 @@ get_differential_transcript_abundance_glmmSeq <- function(.data,
.abundance = enquo(.abundance)
.sample_total_read_count = enquo(.sample_total_read_count)
.dispersion = enquo(.dispersion)

# Check if omit_contrast_in_colnames is correctly setup
if(omit_contrast_in_colnames & length(.contrasts) > 1){
warning("tidybulk says: you can omit contrasts in column names only when maximum one contrast is present")
Expand Down Expand Up @@ -757,27 +757,27 @@ get_differential_transcript_abundance_glmmSeq <- function(.data,

# Reorder counts
counts = counts[,rownames(metadata),drop=FALSE]

if(quo_is_symbolic(.dispersion))
dispersion = .data |> pivot_transcript(!!.transcript) |> select(!!.transcript, !!.dispersion) |> deframe()
else
dispersion = setNames(edgeR::estimateDisp(counts)$tagwise.dispersion, rownames(counts))

# # Check dispersion
# if(!names(dispersion) |> sort() |> identical(
# rownames(counts) |>
# sort()
# )) stop("tidybulk says: The features in the dispersion vector do not overlap with the feature in the assay")

# Make sure the order matches the counts
dispersion = dispersion[rownames(counts)]
glmmSeq_object =

glmmSeq_object =
glmmSeq( .formula,
countdata = counts ,
metadata = metadata,
dispersion = dispersion,
progress = TRUE,
progress = TRUE,
method = method |> str_remove("(?i)^glmmSeq_"),
...
)
Expand Down Expand Up @@ -3974,6 +3974,10 @@ fill_NA_using_value = function(.data,
# filter(how_many_bimod == 0)


#' @details
#' This function plots the GSEA for gene overrepresentation
#'
#'
#' @keywords internal
#' @noRd
#'
Expand Down Expand Up @@ -4031,6 +4035,8 @@ entrez_over_to_gsea = function(my_entrez_rank, species, gene_collections = NULL
}


#' @details
#' This function plots the GSEA for gene overrepresentation
#'
#' @keywords internal
#' @noRd
Expand Down Expand Up @@ -4066,20 +4072,21 @@ entrez_rank_to_gsea = function(my_entrez_rank, species, gene_collections = NULL
}

# Get gene sets signatures
my_gene_collection =
gene_collections %>%
when(
is.null(gene_collections ) ~ msigdbr::msigdbr(species = species) ,
is(., "character") ~ msigdbr::msigdbr(species = species) %>% filter( gs_cat %in% gene_collections ),
is(., "list") ~
tibble(gs_name=names(.), entrez_gene = . ) %>% unnest(entrez_gene) %>% mutate(gs_cat = "user_defined"),
~ stop("tidybulk says: the gene sets should be either a character vector or a named list")
)
my_gene_collection %>%
if(is.null(gene_collections ) )
my_gene_collection = msigdbr::msigdbr(species = species)
else if(gene_collections |> is("character"))
my_gene_collection = msigdbr::msigdbr(species = species) %>% filter( tolower(gs_cat) %in% tolower(gene_collections) )
else if(gene_collections |> is("list"))
my_gene_collection = tibble(gs_name=names(.), entrez_gene = . ) %>% unnest(entrez_gene) %>% mutate(gs_cat = "user_defined")
else
stop("tidybulk says: the gene sets should be either a character vector or a named list")


my_gene_collection |>


# Execute calculation
nest(data = -gs_cat) %>%
nest(data = -gs_cat) |>
mutate(fit =
map(
data,
Expand All @@ -4089,18 +4096,18 @@ entrez_rank_to_gsea = function(my_entrez_rank, species, gene_collections = NULL
pvalueCutoff = 1
)

)) %>%
)) |>
mutate(test =
map(
fit,
~ .x %>%
ggplot2::fortify(showCategory=Inf) %>%
as_tibble() %>%
~ .x |>
# ggplot2::fortify(showCategory=Inf) %>%
as_tibble() |>
rowid_to_column(var = "idx_for_plotting")
#%>%
# mutate(plot = future_imap(ID, ~ enrichplot::gseaplot2(fit, geneSetID = .y, title = .x)))

)) %>%
)) |>
select(-data)


Expand Down
12 changes: 6 additions & 6 deletions R/methods.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3928,10 +3928,10 @@ setGeneric("test_gene_rank", function(.data,
}

# Get column names
.sample = enquo(.sample)
.sample = get_sample(.data, .sample)$.sample
.arrange_desc = enquo(.arrange_desc)
.entrez = enquo(.entrez)
.sample = enquo(.sample)
.sample = get_sample(.data, .sample)$.sample
.arrange_desc = enquo(.arrange_desc)
.entrez = enquo(.entrez)

# Check if ranking is set
if(quo_is_missing(.arrange_desc))
Expand All @@ -3953,13 +3953,13 @@ setGeneric("test_gene_rank", function(.data,
stop(sprintf("tidybulk says: wrong species name. MSigDB uses the latin species names (e.g., %s)", paste(msigdbr::msigdbr_species()$species_name, collapse=", ")))

# Check if missing entrez
if(.data |> filter(!!.entrez |> is.na()) |> nrow() |> gt(0) ){
if(.data |> filter(is.na(!!.entrez)) |> nrow() > 0 ){
warning("tidybulk says: there are .entrez that are NA. Those will be removed")
.data = .data |> filter(!!.entrez |> is.na() |> not())
}

# Check if missing .arrange_desc
if(.data |> filter(!!.arrange_desc |> is.na()) |> nrow() |> gt(0) ){
if(.data |> filter(is.na(!!.arrange_desc)) |> nrow() > 0 ){
warning("tidybulk says: there are .arrange_desc that are NA. Those will be removed")
.data = .data |> filter(!!.arrange_desc |> is.na() |> not())
}
Expand Down