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app update
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@noriakis
noriakis committed Apr 14, 2024
1 parent 17b60cc commit 1afcda4
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14 changes: 11 additions & 3 deletions R/doGSEA.R
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Original file line number Diff line number Diff line change
Expand Up @@ -14,11 +14,13 @@
#' @param zeroPerc genes >= the percentage of count zero sample will be excluded.
#' Default to zero, not recommended in GSEA
#' @param bg_filter filter the background for those in table
#' @param background background TERM2GENE data
#' @importFrom MKmisc mod.t.test
#' @return GSEA results from clusterProfiler
#' @export
doGSEA <- function(stana, candSp=NULL, cl=NULL, eps=1e-2, how=sum,
zeroPerc=0, rankMethod="modt", target="pathway", bg_filter=TRUE) {
zeroPerc=0, rankMethod="modt", target="pathway", bg_filter=TRUE,
background=NULL) {
if (is.null(candSp)) {candSp <- stana@ids[1]}
if (is.null(cl)) {cl <- stana@cl}
if (length(cl)!=2) {stop("Only the two group is supported")}
Expand Down Expand Up @@ -73,8 +75,14 @@ doGSEA <- function(stana, candSp=NULL, cl=NULL, eps=1e-2, how=sum,
kopgsea <- kopgsea[kopgsea$V2 %in% sub, ]
}
## Return all the value regardless of P
enr <- GSEA(ko_sum,
TERM2GENE = kopgsea, pvalueCutoff=1)
if (!is.null(background)) {
enr <- GSEA(ko_sum,
TERM2GENE = background, pvalueCutoff=1)
} else {
enr <- GSEA(ko_sum,
TERM2GENE = kopgsea, pvalueCutoff=1)
}

if (!is.null(stana@gsea[[candSp]])) {
cat_subtle("# Overriding previous GSEA result\n")
}
Expand Down
124 changes: 78 additions & 46 deletions inst/extdata/app_stana.R
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Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,13 @@ library(shiny)
library(shinyjs)
library(shinyWidgets)
library(waiter)

library(dplyr)
library(ggtree)
library(ggplot2)
library(patchwork)
library(RColorBrewer)
library(ggraph)
library(ComplexHeatmap)
library(MicrobiomeProfiler)
library(ggkegg)
library(GetoptLong)
library(ggnewscale)
Expand Down Expand Up @@ -80,15 +79,15 @@ mod.T <- function(mat, l1, l2) {
return_all_gsea_heatmap <- function(list_of_gsea, sel="enrichmentScore",
retTable=FALSE, title="GSEAMat") {
matl <- lapply(names(list_of_gsea), function(x) {
list_of_gsea[[x]]@result |> dplyr::select(ID, sel)
list_of_gsea[[x]] |> dplyr::select(pathway, sel)
})
hm <- matl |>
purrr::reduce(full_join, by = "ID") |>
`colnames<-`(c("ID",names(list_of_gsea))) |>
purrr::reduce(full_join, by = "pathway") |>
`colnames<-`(c("pathway",names(list_of_gsea))) |>
data.frame(check.names=FALSE)

row.names(hm) <- hm$ID
hm$ID <- NULL
row.names(hm) <- hm$pathway
hm$pathway <- NULL
hm2 <- hm |> mutate_all(~as.numeric(.))
changer <- nmls$V2 |> setNames(nmls$V1)
row.names(hm2) <- changer[row.names(hm2)]
Expand Down Expand Up @@ -1145,7 +1144,18 @@ server <- function(input, output, session) {

}
}

## Prepare for the BG set, should be modified if specified in certain environments
kopgsea <- kop
kopgsea <- kopgsea |> filter(startsWith(V1, "path:ko"))
kopgsea$V1 <- kopgsea$V1 |> strsplit(":") |>
vapply("[",2,FUN.VALUE="a")

paths <- unique(kopgsea$V1)
nl <- lapply(paths, function(p) {
tmp <- subset(kopgsea, kopgsea$V1 == p)
tmp$V2
})
names(nl) <- paths
if (input$lfc) {
## Calculate LFC if two variables!
a <- unique(sel_cv)[1]
Expand Down Expand Up @@ -1175,28 +1185,36 @@ server <- function(input, output, session) {
ko_sum <- mod.T(ko_df_filt, aa, bb)
if (is.null(ko_sum)) {waiter_hide(); return(1); showNotification("Matrix is empty.")}
ko_sum <- ko_sum[order(ko_sum, decreasing=TRUE)]
# top50 <- names(abs(ko_sum)[order(abs(ko_sum), decreasing=TRUE)]) |> strsplit(":") |> sapply("[",2)


if (input$gsea) {
updateLog(paste0("Performing GSEA for ", values$sp_id))
kopgsea <- kop
kopgsea <- kopgsea |> filter(startsWith(V1, "path:ko"))
kopgsea$V1 <- kopgsea$V1 |> strsplit(":") |>
vapply("[",2,FUN.VALUE="a")
# if (length(ko_sum)==0) {return(1);waiter_hide();}
enr <- clusterProfiler::GSEA(ko_sum,
TERM2GENE = kopgsea, pvalueCutoff=1)




res <- fgsea::fgsea(nl, ko_sum, nproc=1)
enr <- data.frame(res)

## Changing list to char
enr[[8]] <- unlist(lapply(enr[[8]], function(x) paste0(x, collapse="/")))
enr <- enr[order(enr$padj), ]

} else {
updateLog(paste0("Performing ORA for ", values$sp_id))


if (input$updown) {
candint <- intersect(names(ko_sum[ko_sum>0]), names(apvs[apvs < 0.05])) |>
strsplit(":") |> sapply("[",2)
candint <- intersect(names(ko_sum[ko_sum>0]), names(apvs[apvs < 0.05]))
} else {
candint <- intersect(names(ko_sum[ko_sum<0]), names(apvs[apvs < 0.05])) |>
strsplit(":") |> sapply("[",2)
candint <- intersect(names(ko_sum[ko_sum<0]), names(apvs[apvs < 0.05]))
}
qqcat("Length of candint: @{length(candint)}\n")
if (length(candint)==0) {waiter_hide();return(1);}
enr <- enrichKO(candint, pvalueCutoff=1)

enr <- fgsea::fora(nl, candint, universe=names(ko_sum))

res <- data.frame(enr)
if (is.null(enr)) {waiter_hide();return(1);}
}
} else {
Expand All @@ -1207,18 +1225,19 @@ server <- function(input, output, session) {
strsplit(":") |> sapply("[", 2)
## Performing ORA on all KOs
qqcat("Performing EA\n")
enr <- enrichKO(top50)
enr <- fgsea::fora(nl, top50, names(ko_sum))
res <- data.frame(enr)
}

qqcat("Inserting named vector of values to reactive\n")
if (input$gsea) {
pnames <- nmls$V2 |> setNames(nmls$V1)
enr@result$Description <- pnames[enr@result$Description]
}

pnames <- nmls$V2 |> setNames(nmls$V1)
enr$Description <- pnames[enr$pathway]

values$lfc <- ko_sum
values$enr <- enr
output$showEnr <- DT::renderDataTable(enr@result, caption=comp_label)
all_path <- enr@result[,"Description"]
output$showEnr <- DT::renderDataTable(enr, caption=comp_label)
all_path <- enr$Description
updateSelectInput(session, "path_selector",
choices = all_path)

Expand Down Expand Up @@ -1366,7 +1385,18 @@ server <- function(input, output, session) {

}
}

## Prepare for the BG set, should be modified if specified in certain environments
kopgsea <- kop
kopgsea <- kopgsea |> filter(startsWith(V1, "path:ko"))
kopgsea$V1 <- kopgsea$V1 |> strsplit(":") |>
vapply("[",2,FUN.VALUE="a")

paths <- unique(kopgsea$V1)
nl <- lapply(paths, function(p) {
tmp <- subset(kopgsea, kopgsea$V1 == p)
tmp$V2
})
names(nl) <- paths
if (input$lfc) {
## Calculate LFC if two variables!
## Fix levels for all the comparison
Expand Down Expand Up @@ -1396,16 +1426,18 @@ server <- function(input, output, session) {
# top50 <- names(abs(ko_sum)[order(abs(ko_sum), decreasing=TRUE)]) |> strsplit(":") |> sapply("[",2)
updateLog(paste0("Performing GSEA for ", sp_id))
qqcat("GSEAMat: Cleared the threshold (@{curthre}), performing GSEA for @{sp_id} (@{labnum})\n")
kopgsea <- kop
kopgsea <- kopgsea |> filter(startsWith(V1, "path:ko"))
kopgsea$V1 <- kopgsea$V1 |> strsplit(":") |>
vapply("[",2,FUN.VALUE="a")


if (length(ko_sum)==0) {next;}
withProgress(
enr <- clusterProfiler::GSEA(ko_sum,
TERM2GENE = kopgsea, pvalueCutoff=1),
res <- fgsea::fgsea(nl, ko_sum, nproc=1),
message=paste0("Performing GSEA: ", sp_id)
)

enr <- data.frame(res)

## Changing list to char
enr[[8]] <- unlist(lapply(enr[[8]], function(x) paste0(x, collapse="/")))
## Saving function
# save(file=paste0(input$site,"_",cur_cv,"_",sp,".rda"), enr)
} else {
Expand All @@ -1415,8 +1447,8 @@ server <- function(input, output, session) {
top50 <- names(ko_sum[order(ko_sum, decreasing=TRUE)]) |>
strsplit(":") |> sapply("[", 2)
## Performing ORA on all KOs
qqcat("Performing EA\n")
enr <- enrichKO(top50)
cat_subtle("# Performing EA\n")
enr <- fgsea::fora(nl, top50, names(ko_sum)) %>% data.frame()
}
list_of_gsea[[sp]] <- enr
} else {
Expand Down Expand Up @@ -1459,17 +1491,17 @@ server <- function(input, output, session) {
updateTabsetPanel(session, "main_tab",
selected = "KEGG PATHWAY")
qqcat(" @{input$path_selector}")
enr_res <- values$enr@result
if (startsWith(enr_res$ID[1], "ko")) {
enr_res$ID <- gsub("ko","map",enr_res$ID)
enr_res <- values$enr
if (startsWith(enr_res$pathway[1], "ko")) {
enr_res$pathway <- gsub("ko","map",enr_res$pathway)
}
tmp <- enr_res[ enr_res$Description==input$path_selector, ]

if (startsWith(tmp$ID, "map012") | startsWith(tmp$ID, "map011")) {## If global map
if (startsWith(tmp$pathway, "map012") | startsWith(tmp$pathway, "map011")) {## If global map
if (input$ggraph) {
path <- pathway(gsub("map","ko",tmp$ID), directory="pathways") |> process_reaction()
path <- pathway(gsub("map","ko",tmp$pathway)) |> process_reaction()
} else {
path <- pathway(gsub("map","ko",tmp$ID), directory="pathways") |> process_line()
path <- pathway(gsub("map","ko",tmp$pathway)) |> process_line()
}
path <- path |> activate(edges) |> mutate(num = edge_numeric(values$lfc))
dd <- (path |> activate(edges) |> data.frame())
Expand Down Expand Up @@ -1505,7 +1537,7 @@ server <- function(input, output, session) {

graph <- path |>
ggraph(layout="manual", x=x, y=y) +
overlay_raw_map(directory="pathways", use_cache=FALSE)+
overlay_raw_map()+
geom_edge_link0(aes(color=num))+
scale_edge_color_gradient(low="blue",high="red",name="Statistics")+
theme_void()
Expand All @@ -1514,10 +1546,10 @@ server <- function(input, output, session) {
statdf <- statdf[!duplicated(statdf[,c("ko","num")]),]
}
} else {## If not global map
path <- pathway(gsub("map","ko",tmp$ID), directory="pathways")
path <- pathway(gsub("map","ko",tmp$pathway))
path <- path |> activate(nodes) |> mutate(num = node_numeric(values$lfc),ko=convert_id("ko"))
graph <- ggraph(path, layout="manual", x=x, y=y) +
overlay_raw_map(directory="pathways", use_cache=FALSE)+
overlay_raw_map()+
geom_node_rect(aes(fill=num, filter=type=="ortholog"),
color="black")+
geom_node_text(aes(label=strsplit(graphics_name, ",") %>%
Expand Down
5 changes: 4 additions & 1 deletion man/doGSEA.Rd
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