R/create_signs.R
In keita-iida/ASURATBI: A pipeline especially built for computing several single-cell datasets
Defines functions
makeSignMatrix
select_signs_manually
remove_signs_manually
remove_signs_redundant
create_signs
cluster_genesets
remove_signs
Documented in
cluster_genesets
create_signs
makeSignMatrix
remove_signs
remove_signs_manually
remove_signs_redundant
select_signs_manually
#-----------------------------------------------------------------------------80
#
#-----------------------------------------------------------------------------80
#' Remove signs including too few or too many genes.
#'
#' This function removes signs including too few or too many genes.
#'
#' @param sce A SingleCellExperiment object.
#' @param min_ngenes Minimum number of genes, which must be greater than one.
#' @param max_ngenes Maximum number of genes, which must be greater than one.
#'
#' @return A SingleCellExperiment object.
#' @import SingleCellExperiment
#' @import SummarizedExperiment
#' @import S4Vectors
#' @export
#'
#' @examples
#' data(pbmc_eg)
#' data(human_GO_eg)
#' pbmcs <- list(GO = pbmc_eg)
#' S4Vectors::metadata(pbmcs$GO) <- list(sign = human_GO_eg[["BP"]])
#' pbmcs$GO <- remove_signs(sce = pbmcs$GO, min_ngenes = 2, max_ngenes = 1000)
#' # The results are stored in `metadata(pbmcs$GO)$sign`.
#'
remove_signs <- function(sce = NULL, min_ngenes = 2, max_ngenes = 1000){
#--------------------------------------------------
# Error handling
#--------------------------------------------------
if(is.null(metadata(sce)$sign)){
stop("metadata(sce)$sign must have a database.")
}
if(min_ngenes <= 1){ stop("min_ngenes should be >= 2.") }
if(max_ngenes <= 1){ stop("max_ngenes should be >= 2.") }
#--------------------------------------------------
# Select innate genes.
#--------------------------------------------------
innate_g <- data.frame(gene = rownames(sce), geneID = rowData(sce)$geneID)
tmp <- metadata(sce)$sign
for(i in seq_len(nrow(tmp))){
#------------------------------
# GeneID: ENTREZ Gene ID
#------------------------------
geneIDs <- unlist(strsplit(tmp$GeneID[i], "/"))
geneIDs <- geneIDs[which(geneIDs %in% innate_g$geneID)]
tmp$GeneID[i] <- paste(geneIDs, collapse = "/")
#------------------------------
# Gene: gene symbol
#------------------------------
genes <- c()
for(j in seq_len(length(geneIDs))){
genes <- c(genes, innate_g[which(innate_g$geneID == geneIDs[j]), ]$gene)
}
tmp$Gene[i] <- paste(genes, collapse = "/")
#------------------------------
# Count
#------------------------------
tmp$Count[i] <- as.integer(length(geneIDs))
}
metadata(sce)$sign <- tmp
#--------------------------------------------------
# Remove IDs including too few or too many genes.
#--------------------------------------------------
tmp <- metadata(sce)$sign
res <- tmp[which((tmp$Count >= min_ngenes) & (tmp$Count <= max_ngenes)), ]
rownames(res) <- seq_len(nrow(res))
metadata(sce)$sign <- as.data.frame(res)
return(sce)
}
#-----------------------------------------------------------------------------80
#
#-----------------------------------------------------------------------------80
#' Cluster each functional gene set into three groups.
#'
#' This function clusters each functional gene set into strongly, variably, and
#' weakly correlated gene sets.
#'
#' @param sce A SingleCellExperiment object.
#' @param cormat A correlation matrix of gene expressions.
#' @param th_posi A threshold of positive correlation coefficient.
#' @param th_nega A threshold of negative correlation coefficient.
#'
#' @return A SingleCellExperiment object.
#' @import SingleCellExperiment
#' @import SummarizedExperiment
#' @import S4Vectors
#' @importFrom cluster pam
#' @export
#'
#' @examples
#' data(pbmc_eg)
#' data(human_GO_eg)
#' mat <- t(as.matrix(SummarizedExperiment::assay(pbmc_eg, "centered")))
#' pbmc_cormat <- cor(mat, method = "spearman")
#' pbmcs <- list(GO = pbmc_eg)
#' S4Vectors::metadata(pbmcs$GO) <- list(sign = human_GO_eg[["BP"]])
#' pbmcs$GO <- remove_signs(sce = pbmcs$GO, min_ngenes = 2, max_ngenes = 1000)
#' pbmcs$GO <- cluster_genesets(sce = pbmcs$GO, cormat = pbmc_cormat,
#' th_posi = 0.24, th_nega = -0.20)
#' # The results are stored in `metadata(pbmcs$GO)$sign`.
#'
cluster_genesets <- function(
sce = NULL, cormat = NULL, th_posi = NULL, th_nega = NULL
){
#--------------------------------------------------
# Error handling
#--------------------------------------------------
if(th_posi < 0){ stop("th_posi should be >= 0.") }
if(th_nega > 0){ stop("th_nega should be <= 0.") }
#--------------------------------------------------
# Correlation graph-based decomposition of FGSs
#--------------------------------------------------
df <- metadata(sce)$sign
res <- c("SignID", "Description", "IC",
"CountStrgCorrGene", "CountVariCorrGene", "CountWeakCorrGene",
"CorrStrg", "CorrVari", "CorrWeak",
"StrgCorrGene", "VariCorrGene", "WeakCorrGene",
"StrgCorrGeneID", "VariCorrGeneID", "WeakCorrGeneID")
res <- data.frame(matrix(ncol = 15, nrow = 0, dimnames = list(NULL, res)))
for(i in seq_len(nrow(df))){
genes <- unlist(strsplit(df$Gene[i], "/"))
if(length(genes) <= 1){
next
}
inds <- which(rownames(cormat) %in% genes)
if(length(inds) <= 2){
next
}
mat <- cormat[inds, inds]
#--------------------------------------------------
# Select genes having strong correlations with others.
#--------------------------------------------------
diag(mat) <- -99
inds_posi <- which(apply(mat, 2, function(x) sum(x >= th_posi)) > 0)
diag(mat) <- 99
inds_nega <- which(apply(mat, 2, function(x) sum(x <= th_nega)) > 0)
if(length(inds_posi) == 0){
#--------------------------------------------------
# Define strongly, variably, and weakly correlated gene sets.
#--------------------------------------------------
genes_strg <- NA ; genes_vari <- NA ; genes_weak <- genes
mean_strg <- NA ; mean_vari <- NA
mean_weak <- ifelse(length(genes_weak) <= 1, NA, mean(mat[mat <= 1]))
}else{
if(length(inds_nega) == 0){
#--------------------------------------------------
# Define strongly, variably, and weakly correlated gene sets.
#--------------------------------------------------
genes_vari <- NA ; mean_vari <- NA
submat <- mat[inds_posi, inds_posi]
genes_strg <- rownames(submat)
mean_strg <- ifelse(length(genes_strg) <= 1, NA,
mean(submat[submat <= 1]))
if(mean_strg < th_posi){
genes_strg <- NA ; mean_strg <- NA
genes_weak <- genes
mean_weak <- ifelse(length(genes_weak) <= 1, NA, mean(mat[mat <= 1]))
}else{
genes_weak <- setdiff(genes, genes_strg)
inds <- which(rownames(mat) %in% genes_weak)
tmp <- mat[inds, inds]
mean_weak <- ifelse(length(inds) <= 1, NA, mean(tmp[tmp <= 1]))
}
}else{
inds <- union(inds_posi, inds_nega)
submat <- mat[inds, inds] ; diag(submat) <- 1
#--------------------------------------------------
# PAM clustering using cluster package
#--------------------------------------------------
c <- pam(submat, k = 2)
diag(submat) <- 99
gset <- list() ; mu <- c()
for(j in seq_len(2)){
gset[[j]] <- names(c[["clustering"]])[which(c[["clustering"]] == j)]
inds <- which(rownames(submat) %in% gset[[j]])
tmp <- submat[inds, inds]
mu[j] <- ifelse(length(inds) <= 1, NA, mean(tmp[tmp <= 1]))
}
#--------------------------------------------------
# Define strongly, variably, and weakly correlated gene sets.
#--------------------------------------------------
inds <- order(mu, decreasing = TRUE)
genes_strg <- gset[[inds[1]]]
mean_strg <- mu[inds[1]]
if(mean_strg < th_posi){
genes_strg <- NA ; mean_strg <- NA
genes_vari <- NA ; mean_vari <- NA
genes_weak <- genes
mean_weak <- ifelse(length(genes_weak) <= 1, NA, mean(mat[mat <= 1]))
}else{
genes_vari <- gset[[inds[2]]]
mean_vari <- mu[inds[2]]
genes_weak <- setdiff(genes, union(gset[[1]], gset[[2]]))
inds <- which(rownames(mat) %in% genes_weak)
tmp <- mat[inds, inds]
mean_weak <- ifelse(length(inds) <= 1, NA, mean(tmp[tmp <= 1]))
}
}
}
#--------------------------------------------------
# Result
#--------------------------------------------------
tmp <- as.data.frame(rowData(sce))
if(is.element(NA, genes_strg)){
genes_strg <- NA ; geneIDs_strg <- NA ; count_strg <- 0
}else{
count_strg <- length(genes_strg)
gs <- c()
for(j in seq_along(genes_strg)){
inds <- which(rownames(tmp) == genes_strg[j])
if(ncol(tmp) == 1){
if(colnames(tmp) == "geneID"){
gs <- c(gs, tmp[inds, ])
}else{
stop("rowData() has only one column; the name must be \"geneID\".")
}
}else{
gs <- c(gs, tmp[inds, ]$geneID)
}
}
geneIDs_strg <- paste(gs, collapse = "/")
genes_strg <- paste(genes_strg, collapse = "/")
}
if(is.element(NA, genes_vari)){
genes_vari <- NA ; geneIDs_vari <- NA ; count_vari <- 0
}else{
count_vari <- length(genes_vari)
gs <- c()
for(j in seq_along(genes_vari)){
inds <- which(rownames(tmp) == genes_vari[j])
if(ncol(tmp) == 1){
if(colnames(tmp) == "geneID"){
gs <- c(gs, tmp[inds, ])
}else{
stop("rowData() has only one column; the name must be \"geneID\".")
}
}else{
gs <- c(gs, tmp[inds, ]$geneID)
}
}
geneIDs_vari <- paste(gs, collapse = "/")
genes_vari <- paste(genes_vari, collapse = "/")
}
if(is.element(NA, genes_weak)){
genes_weak <- NA ; geneIDs_weak <- NA ; count_weak <- 0
}else{
count_weak <- length(genes_weak)
gs <- c()
for(j in seq_along(genes_weak)){
inds <- which(rownames(tmp) == genes_weak[j])
if(ncol(tmp) == 1){
if(colnames(tmp) == "geneID"){
gs <- c(gs, tmp[inds, ])
}else{
stop("rowData() has only one column; the name must be \"geneID\".")
}
}else{
gs <- c(gs, tmp[inds, ]$geneID)
}
}
geneIDs_weak <- paste(gs, collapse = "/")
genes_weak <- paste(genes_weak, collapse = "/")
}
dg <- data.frame(SignID = df$ID[i], Description = df$Description[i],
IC = df$IC[i],
CountStrgCorrGene = count_strg,
CountVariCorrGene = count_vari,
CountWeakCorrGene = count_weak,
CorrStrg = mean_strg,
CorrVari = mean_vari,
CorrWeak = mean_weak,
StrgCorrGene = genes_strg,
VariCorrGene = genes_vari,
WeakCorrGene = genes_weak,
StrgCorrGeneID = geneIDs_strg,
VariCorrGeneID = geneIDs_vari,
WeakCorrGeneID = geneIDs_weak)
res <- rbind(res, dg)
}
metadata(sce)$sign <- res
return(sce)
}
#-----------------------------------------------------------------------------80
#
#-----------------------------------------------------------------------------80
#' Define signs for strongly and variably correlated gene sets.
#'
#' This function define signs for strongly and variably correlated gene sets.
#'
#' @param sce A SingleCellExperiment object.
#' @param min_cnt_strg An integer for the cutoff value for strongly correlated
#' gene sets.
#' @param min_cnt_vari An integer for the cutoff value for variably correlated
#' gene sets.
#'
#' @return A SingleCellExperiment object.
#' @import SingleCellExperiment
#' @import SummarizedExperiment
#' @import S4Vectors
#' @export
#'
#' @examples
#' data(pbmc_eg)
#' data(human_GO_eg)
#' mat <- t(as.matrix(SummarizedExperiment::assay(pbmc_eg, "centered")))
#' pbmc_cormat <- cor(mat, method = "spearman")
#' pbmcs <- list(GO = pbmc_eg)
#' S4Vectors::metadata(pbmcs$GO) <- list(sign = human_GO_eg[["BP"]])
#' pbmcs$GO <- remove_signs(sce = pbmcs$GO, min_ngenes = 2, max_ngenes = 1000)
#' pbmcs$GO <- cluster_genesets(sce = pbmcs$GO, cormat = pbmc_cormat,
#' th_posi = 0.24, th_nega = -0.20)
#' pbmcs$GO <- create_signs(sce = pbmcs$GO, min_cnt_strg = 2, min_cnt_vari = 2)
#' # The results are stored in `metadata(pbmcs$GO)$sign_all`.
#'
create_signs <- function(sce = NULL, min_cnt_strg = 2, min_cnt_vari = 2){
#--------------------------------------------------
# Error handling
#--------------------------------------------------
if(min_cnt_strg <= 0){ stop("min_cnt_strg should be >= 1.") }
if(min_cnt_vari <= 0){ stop("min_cnt_vari should be >= 1.") }
df <- metadata(sce)$sign
#--------------------------------------------------
# Strongly correlated gene sets
#--------------------------------------------------
df_strg <- df[which(df$CountStrgCorrGene >= min_cnt_strg), ]
if(nrow(df_strg) >= 1){
df_strg <- data.frame(
SignID = df_strg$SignID, Description = df_strg$Description,
IC = df_strg$IC,
CountStrgCorrGene = df_strg$CountStrgCorrGene,
CountWeakCorrGene = df_strg$CountWeakCorrGene,
CorrStrg = df_strg$CorrStrg, CorrWeak = df_strg$CorrWeak,
StrgCorrGene = df_strg$StrgCorrGene, WeakCorrGene = df_strg$WeakCorrGene,
StrgCorrGeneID = df_strg$StrgCorrGeneID,
WeakCorrGeneID = df_strg$WeakCorrGeneID)
}
#--------------------------------------------------
# Variably correlated gene sets
#--------------------------------------------------
df_vari <- df[which(df$CountVariCorrGene >= min_cnt_vari), ]
if(nrow(df_vari) >= 1){
df_vari <- data.frame(
SignID = df_vari$SignID, Description = df_vari$Description,
IC = df_vari$IC,
CountVariCorrGene = df_vari$CountVariCorrGene,
CountWeakCorrGene = df_vari$CountWeakCorrGene,
CorrVari = df_vari$CorrVari, CorrWeak = df_vari$CorrWeak,
VariCorrGene = df_vari$VariCorrGene, WeakCorrGene = df_vari$WeakCorrGene,
VariCorrGeneID = df_vari$VariCorrGeneID,
WeakCorrGeneID = df_vari$WeakCorrGeneID)
}
#--------------------------------------------------
# Store the results.
#--------------------------------------------------
metadata(sce)$sign_SCG <- df_strg
metadata(sce)$sign_VCG <- df_vari
#--------------------------------------------------
# Add metadata(sce)$sign_all.
#--------------------------------------------------
metadata(sce)$sign <- NULL
tmp <- c("SignID", "Description", "IC",
"CountCorrGene", "CountWeakCorrGene", "Corr", "CorrWeak",
"CorrGene", "WeakCorrGene", "CorrGeneID", "WeakCorrGeneID")
colnames(df_strg) <- tmp
colnames(df_vari) <- tmp
if(nrow(df_strg) == 0){
stop("SCG is not defined.")
}else{
if(nrow(df_vari) == 0){
metadata(sce)$sign_all <- cbind(CorrType = "SCG", df_strg)
}else{
metadata(sce)$sign_all <- rbind(cbind(CorrType = "SCG", df_strg),
cbind(CorrType = "VCG", df_vari))
}
}
return(sce)
}
#-----------------------------------------------------------------------------80
#
#-----------------------------------------------------------------------------80
#' Remove redundant signs using semantic similarity matrices.
#'
#' This function removes redundant signs using semantic similarity matrices.
#'
#' @param sce A SingleCellExperiment object.
#' @param similarity_matrix A semantic similarity matrix.
#' @param threshold A threshold value of semantic similarity, used for
#' regarding biological terms as similar ones
#' @param keep_rareID If TRUE, biological terms with the larger ICs are kept.
#'
#' @return A SingleCellExperiment object.
#' @import SingleCellExperiment
#' @import SummarizedExperiment
#' @import S4Vectors
#' @export
#'
#' @examples
#' data(pbmc_eg)
#' data(human_GO_eg)
#' mat <- t(as.matrix(SummarizedExperiment::assay(pbmc_eg, "centered")))
#' pbmc_cormat <- cor(mat, method = "spearman")
#' pbmcs <- list(GO = pbmc_eg)
#' S4Vectors::metadata(pbmcs$GO) <- list(sign = human_GO_eg[["BP"]])
#' pbmcs$GO <- remove_signs(sce = pbmcs$GO, min_ngenes = 2, max_ngenes = 1000)
#' pbmcs$GO <- cluster_genesets(sce = pbmcs$GO, cormat = pbmc_cormat,
#' th_posi = 0.24, th_nega = -0.20)
#' pbmcs$GO <- create_signs(sce = pbmcs$GO, min_cnt_strg = 2, min_cnt_vari = 2)
#' pbmcs$GO <- remove_signs_redundant(
#' sce = pbmcs$GO, similarity_matrix = human_GO_eg$similarity_matrix$BP,
#' threshold = 0.80, keep_rareID = TRUE)
#' # The results are stored in `metadata(pbmcs$GO)$sign_SCG`,
#' # `metadata(pbmcs$GO)$sign_VCG`, `metadata(pbmcs$GO)$sign_all`,
#' # and if there exist, `metadata(pbmcs$GO)$sign_SCG_redundant` and
#' # `metadata(pbmcs$GO)$sign_VCG_redundant`.
#'
remove_signs_redundant <- function(
sce = NULL, similarity_matrix = NULL, threshold = NULL, keep_rareID = NULL
){
#--------------------------------------------------
# Error handling
#--------------------------------------------------
if(is.null(similarity_matrix)){
stop("Semantic similarity is not defined. Skip this process.")
}
report <- list()
s_or_v <- c("sign_SCG", "sign_VCG")
for(k in seq_along(s_or_v)){
#--------------------------------------------------
# Report format
#--------------------------------------------------
df <- metadata(sce)[[s_or_v[k]]]
df <- df[!(is.na(df$IC)), ]
if(nrow(df) == 0){
next
}
inds <- which(rownames(similarity_matrix) %in% df$SignID)
if(length(inds) < 2){
next
}
submat <- similarity_matrix[inds, inds]
inds <- order(df$IC, decreasing = FALSE)
submat <- submat[inds, inds]
report[[k]] <- c("Similarity", "Kept_SignID", "Removed_SignID",
"Kept_Description", "Removed_Description",
"Kept_GeneCount", "Removed_GeneCount",
"Kept_Gene", "Removed_Gene", "Kept_IC", "Removed_IC")
report[[k]] <- data.frame(matrix(ncol = 11, nrow = 0,
dimnames = list(NULL, report[[k]])))
flag <- rep(0, dim(submat)[1])
if(keep_rareID == TRUE){
#--------------------------------------------------
# case I
#--------------------------------------------------
I <- dim(submat)[1]
for(i in seq(I, 2)){
J <- dim(submat)[2] - (I - i + 1) # Be careful
if(flag[i] == 1){ # Be careful
next
}
for(j in seq_len(J)){
if(is.na(submat[i, j])){
next
}
if(abs(submat[i, j]) >= threshold){
ind_kept <- which(df$SignID == rownames(submat)[i])
ind_remo <- which(df$SignID == rownames(submat)[j])
if(k == 1){
kept_count <- df[ind_kept, ]$CountStrgCorrGene +
df[ind_kept, ]$CountWeakCorrGene
remo_count <- df[ind_remo, ]$CountStrgCorrGene +
df[ind_remo, ]$CountWeakCorrGene
kept_genes <- paste(df[ind_kept, ]$StrgCorrGene,
df[ind_kept, ]$WeakCorrGene, sep = "/")
remo_genes <- paste(df[ind_remo, ]$StrgCorrGene,
df[ind_remo, ]$WeakCorrGene, sep = "/")
}else if(k == 2){
kept_count <- df[ind_kept, ]$CountVariCorrGene +
df[ind_kept, ]$CountWeakCorrGene
remo_count <- df[ind_remo, ]$CountVariCorrGene +
df[ind_remo, ]$CountWeakCorrGene
kept_genes <- paste(df[ind_kept, ]$VariCorrGene,
df[ind_kept, ]$WeakCorrGene, sep = "/")
remo_genes <- paste(df[ind_remo, ]$VariCorrGene,
df[ind_remo, ]$WeakCorrGene, sep = "/")
}
report[[k]] <- rbind(report[[k]], data.frame(
Similarity = submat[i, j],
Kept_SignID = df[ind_kept, ]$SignID,
Removed_SignID = df[ind_remo, ]$SignID,
Kept_Description = df[ind_kept, ]$Description,
Removed_Description = df[ind_remo, ]$Description,
Kept_GeneCount = kept_count,
Removed_GeneCount = remo_count,
Kept_Gene = kept_genes,
Removed_Gene = remo_genes,
Kept_IC = df[ind_kept, ]$IC,
Removed_IC = df[ind_remo, ]$IC
))
flag[j] <- 1
}
}
}
}else{
#--------------------------------------------------
# case II
#--------------------------------------------------
I <- dim(submat)[1] - 1
J <- dim(submat)[2]
for(i in seq_len(I)){
j0 <- i + 1 # Be careful
if(flag[i] == 1){ # Be careful
next
}
for(j in seq(j0, J)){
if(is.na(submat[i, j])){
next
}
if(abs(submat[i, j]) >= threshold){
ind_kept <- which(df$SignID == rownames(submat)[i])
ind_remo <- which(df$SignID == rownames(submat)[j])
if(k == 1){
kept_count <- df[ind_kept, ]$CountStrgCorrGene +
df[ind_kept, ]$CountWeakCorrGene
remo_count <- df[ind_remo, ]$CountStrgCorrGene +
df[ind_remo, ]$CountWeakCorrGene
kept_genes <- paste(df[ind_kept, ]$StrgCorrGene,
df[ind_kept, ]$WeakCorrGene, sep = "/")
remo_genes <- paste(df[ind_remo, ]$StrgCorrGene,
df[ind_remo, ]$WeakCorrGene, sep = "/")
}else if(k == 2){
kept_count <- df[ind_kept, ]$CountVariCorrGene +
df[ind_kept, ]$CountWeakCorrGene
remo_count <- df[ind_remo, ]$CountVariCorrGene +
df[ind_remo, ]$CountWeakCorrGene
kept_genes <- paste(df[ind_kept, ]$VariCorrGene,
df[ind_kept, ]$WeakCorrGene, sep = "/")
remo_genes <- paste(df[ind_remo, ]$VariCorrGene,
df[ind_remo, ]$WeakCorrGene, sep = "/")
}
report[[k]] <- rbind(report[[k]], data.frame(
Similarity = submat[i, j],
Kept_SignID = df[ind_kept, ]$SignID,
Removed_SignID = df[ind_remo, ]$SignID,
Kept_Description = df[ind_kept, ]$Description,
Removed_Description = df[ind_remo, ]$Description,
Kept_GeneCount = kept_count,
Removed_GeneCount = remo_count,
Kept_Gene = kept_genes,
Removed_Gene = remo_genes,
Kept_IC = df[ind_kept, ]$IC,
Removed_IC = df[ind_remo, ]$IC
))
flag[j] <- 1
}
}
}
}
#--------------------------------------------------
# Remove redundant signs.
#--------------------------------------------------
if(length(report[[k]]$Removed_SignID) >= 1){
kept_IDs <- setdiff(df$SignID, report[[k]]$Removed_SignID)
res <- df[which(df$SignID %in% kept_IDs), ]
rownames(res) <- seq_len(nrow(res))
}else{
res <- df
}
metadata(sce)[[s_or_v[k]]] <- res
}
#--------------------------------------------------
# Modify metadata(sce)$sign_all.
#--------------------------------------------------
df_strg <- as.data.frame(metadata(sce)$sign_SCG)
df_vari <- as.data.frame(metadata(sce)$sign_VCG)
tmp <- c("SignID", "Description", "IC",
"CountCorrGene", "CountWeakCorrGene", "Corr", "CorrWeak",
"CorrGene", "WeakCorrGene", "CorrGeneID", "WeakCorrGeneID")
colnames(df_strg) <- tmp
colnames(df_vari) <- tmp
if(nrow(df_strg) == 0){
stop("SCG is not defined.")
}else{
if(nrow(df_vari) == 0){
metadata(sce)$sign_all <- cbind(CorrType = "SCG", df_strg)
}else{
metadata(sce)$sign_all <- rbind(cbind(CorrType = "SCG", df_strg),
cbind(CorrType = "VCG", df_vari))
}
}
#--------------------------------------------------
# Store the report.
#--------------------------------------------------
for(k in seq_along(s_or_v)){
if(nrow(metadata(sce)[[s_or_v[k]]]) < 2){
next
}
text <- paste(s_or_v[k], "redundant", sep = "_")
metadata(sce)[[text]] <- report[[k]]
}
return(sce)
}
#-----------------------------------------------------------------------------80
#
#-----------------------------------------------------------------------------80
#' Remove signs by specifying keywords.
#'
#' This function removes signs by specifying keywords.
#'
#' @param sce A SingleCellExperiment object.
#' @param keywords keywords separated by pipes `|`.
#'
#' @return A SingleCellExperiment object.
#' @import SingleCellExperiment
#' @import SummarizedExperiment
#' @import S4Vectors
#' @export
#'
#' @examples
#' data(pbmc_eg)
#' data(human_GO_eg)
#' mat <- t(as.matrix(SummarizedExperiment::assay(pbmc_eg, "centered")))
#' pbmc_cormat <- cor(mat, method = "spearman")
#' pbmcs <- list(GO = pbmc_eg)
#' S4Vectors::metadata(pbmcs$GO) <- list(sign = human_GO_eg[["BP"]])
#' pbmcs$GO <- remove_signs(sce = pbmcs$GO, min_ngenes = 2, max_ngenes = 1000)
#' pbmcs$GO <- cluster_genesets(sce = pbmcs$GO, cormat = pbmc_cormat,
#' th_posi = 0.24, th_nega = -0.20)
#' pbmcs$GO <- create_signs(sce = pbmcs$GO, min_cnt_strg = 2, min_cnt_vari = 2)
#' keywords <- "Covid19|foofoo|hogehoge"
#' pbmcs$GO <- remove_signs_manually(sce = pbmcs$GO, keywords = keywords)
#' # The results are stored in `metadata(pbmcs$GO)$sign_SCG`,
#' # `metadata(pbmcs$GO)$sign_VCG`, and `metadata(pbmcs$GO)$sign_all`.
#'
remove_signs_manually <- function(sce = NULL, keywords = NULL){
if(is.null(keywords)){
return(sce)
}
s_or_v <- c("sign_SCG", "sign_VCG")
for(k in seq_along(s_or_v)){
df <- metadata(sce)[[s_or_v[k]]]
if(nrow(df) != 0){
tmp <- ((grepl(keywords, df$SignID)) | (grepl(keywords, df$Description)))
df <- df[!tmp, ]
rownames(df) <- seq_len(nrow(df))
}
metadata(sce)[[s_or_v[k]]] <- df
}
#--------------------------------------------------
# Modify metadata(sce)$sign_all.
#--------------------------------------------------
df_strg <- as.data.frame(metadata(sce)$sign_SCG)
df_vari <- as.data.frame(metadata(sce)$sign_VCG)
tmp <- c("SignID", "Description", "IC",
"CountCorrGene", "CountWeakCorrGene", "Corr", "CorrWeak",
"CorrGene", "WeakCorrGene", "CorrGeneID", "WeakCorrGeneID")
colnames(df_strg) <- tmp
colnames(df_vari) <- tmp
if(nrow(df_strg) == 0){
stop("SCG is not defined.")
}else{
if(nrow(df_vari) == 0){
metadata(sce)$sign_all <- cbind(CorrType = "SCG", df_strg)
}else{
metadata(sce)$sign_all <- rbind(cbind(CorrType = "SCG", df_strg),
cbind(CorrType = "VCG", df_vari))
}
}
return(sce)
}
#-----------------------------------------------------------------------------80
#
#-----------------------------------------------------------------------------80
#' Select signs by specifying keywords.
#'
#' This function selects signs by specifying keywords.
#'
#' @param sce An ASURAT object.
#' @param keywords Keywords separated by a pipe.
#'
#' @return An ASURAT object.
#' @import SingleCellExperiment
#' @import SummarizedExperiment
#' @import S4Vectors
#' @export
#'
#' @examples
#' data(pbmc_eg)
#' data(human_GO_eg)
#' mat <- t(as.matrix(SummarizedExperiment::assay(pbmc_eg, "centered")))
#' pbmc_cormat <- cor(mat, method = "spearman")
#' pbmcs <- list(GO = pbmc_eg)
#' S4Vectors::metadata(pbmcs$GO) <- list(sign = human_GO_eg[["BP"]])
#' pbmcs$GO <- remove_signs(sce = pbmcs$GO, min_ngenes = 2, max_ngenes = 1000)
#' pbmcs$GO <- cluster_genesets(sce = pbmcs$GO, cormat = pbmc_cormat,
#' th_posi = 0.24, th_nega = -0.20)
#' pbmcs$GO <- create_signs(sce = pbmcs$GO, min_cnt_strg = 2, min_cnt_vari = 2)
#' keywords <- "cell|process"
#' pbmcs$GO <- select_signs_manually(sce = pbmcs$GO, keywords = keywords)
#' # The results are stored in `metadata(pbmcs$GO)$sign_SCG`,
#' # `metadata(pbmcs$GO)$sign_VCG`, and `metadata(pbmcs$GO)$sign_all`.
#'
select_signs_manually <- function(sce = NULL, keywords = NULL){
if(is.null(keywords)){
return(sce)
}
s_or_v <- c("sign_SCG", "sign_VCG")
for(k in seq_along(s_or_v)){
df <- metadata(sce)[[s_or_v[k]]]
if(nrow(df) != 0){
tmp <- ((grepl(keywords, df$SignID)) | (grepl(keywords, df$Description)))
df <- df[tmp, ]
rownames(df) <- seq_len(nrow(df))
}
metadata(sce)[[s_or_v[k]]] <- df
}
#--------------------------------------------------
# Modify metadata(sce)$sign_all.
#--------------------------------------------------
df_strg <- as.data.frame(metadata(sce)$sign_SCG)
df_vari <- as.data.frame(metadata(sce)$sign_VCG)
tmp <- c("SignID", "Description", "IC",
"CountCorrGene", "CountWeakCorrGene", "Corr", "CorrWeak",
"CorrGene", "WeakCorrGene", "CorrGeneID", "WeakCorrGeneID")
colnames(df_strg) <- tmp
colnames(df_vari) <- tmp
if(nrow(df_strg) == 0){
stop("SCG is not defined. The keywords may not be included in the data.")
}else{
if(nrow(df_vari) == 0){
metadata(sce)$sign_all <- cbind(CorrType = "SCG", df_strg)
}else{
metadata(sce)$sign_all <- rbind(cbind(CorrType = "SCG", df_strg),
cbind(CorrType = "VCG", df_vari))
}
}
return(sce)
}
#-----------------------------------------------------------------------------80
#
#-----------------------------------------------------------------------------80
#' Create a new SingleCellExperiment object for sign-by-sample matrices.
#'
#' This function creates a new SingleCellExperiment object for sign-by-sample
#' matrices (SSM) by concatenating SSMs for strongly and variably correlated
#' gene sets.
#'
#' @param sce A SingleCellExperiment object.
#' @param weight_strg A weight parameter for strongly correlated gene sets.
#' @param weight_vari A weight parameter for variably correlated gene sets.
#'
#' @return A SingleCellExperiment object.
#' @import SingleCellExperiment
#' @import SummarizedExperiment
#' @import S4Vectors
#' @export
#'
#' @examples
#' data(pbmc_eg)
#' data(human_GO_eg)
#' mat <- t(as.matrix(SummarizedExperiment::assay(pbmc_eg, "centered")))
#' pbmc_cormat <- cor(mat, method = "spearman")
#' pbmcs <- list(GO = pbmc_eg)
#' S4Vectors::metadata(pbmcs$GO) <- list(sign = human_GO_eg[["BP"]])
#' pbmcs$GO <- remove_signs(sce = pbmcs$GO, min_ngenes = 2, max_ngenes = 1000)
#' pbmcs$GO <- cluster_genesets(sce = pbmcs$GO, cormat = pbmc_cormat,
#' th_posi = 0.24, th_nega = -0.20)
#' pbmcs$GO <- create_signs(sce = pbmcs$GO, min_cnt_strg = 2, min_cnt_vari = 2)
#' pbmcs$GO <- makeSignMatrix(sce = pbmcs$GO, weight_strg = 0.5,
#' weight_vari = 0.5)
#' # The resutls can be check by, e.g., assay(pbmcs$GO, "counts").
#'
makeSignMatrix <- function(sce = NULL, weight_strg = 0.5, weight_vari = 0.5){
#--------------------------------------------------
# Error handling
#--------------------------------------------------
if((weight_strg == 99) & (weight_strg == 99)){
message("Search a way to bring harmony.")
}
if((weight_strg < 0) | (weight_strg > 1) |
(weight_vari < 0) | (weight_vari > 1)){
stop("weight_* must be values in [0, 1].")
}
mat <- assay(sce, "centered")
res <- matrix(ncol = dim(mat)[2], nrow = 0,
dimnames = list(NULL, colnames(mat)))
rowdata <- c("ParentSignID", "Description", "CorrGene", "WeakCorrGene", "IC")
rowdata <- matrix(ncol = 5, nrow = 0, dimnames = list(NULL, rowdata))
s_or_v <- c("sign_SCG", "sign_VCG")
for(k in seq_along(s_or_v)){
df <- metadata(sce)[[s_or_v[k]]]
if(nrow(df) != 0){
for(i in seq_len(nrow(df))){
#--------------------------------------------------
# Create a sign-by-sample matrix for weakly correlated gene sets
#--------------------------------------------------
if(df$CountWeakCorrGene[i] == 0){
vector_weak <- matrix(0, ncol = dim(mat)[2], nrow = 1,
dimnames = list(NULL, colnames(mat)))
}else{
genes_weak <- unlist(strsplit(df$WeakCorrGene[i], "/"))
submat_weak <- matrix(ncol = dim(mat)[2], nrow = 0,
dimnames = list(NULL, colnames(mat)))
inds <- which(rownames(mat) %in% genes_weak)
submat_weak <- rbind(submat_weak, mat[inds, ])
vector_weak <- apply(submat_weak, 2, mean)
}
#--------------------------------------------------
# Create a sign-by-sample matrix for strongly correlated gene sets
#--------------------------------------------------
if(is.null(df$CountStrgCorrGene[i])){
ssm_strg <- NA
}else{
if(df$CountStrgCorrGene[i] == 0){
vector_strg <- matrix(0, ncol = dim(mat)[2], nrow = 1,
dimnames = list(NULL, colnames(mat)))
}else{
genes_strg <- unlist(strsplit(df$StrgCorrGene[i], "/"))
submat_strg <- matrix(ncol = dim(mat)[2], nrow = 0,
dimnames = list(NULL, colnames(mat)))
inds <- which(rownames(mat) %in% genes_strg)
submat_strg <- rbind(submat_strg, mat[inds, ])
vector_strg <- apply(submat_strg, 2, mean)
}
ssm_strg <- matrix(ncol = dim(mat)[2], nrow = 0,
dimnames = list(NULL, colnames(mat)))
tmp <- weight_strg * vector_strg + (1.0 - weight_strg) * vector_weak
ssm_strg <- rbind(ssm_strg, tmp)
rownames(ssm_strg) <- paste(df$SignID[i], "-", "S", sep = "")
res <- rbind(res, ssm_strg)
tmp <- data.frame(ParentSignID = df$SignID[i],
Description = df$Description[i],
CorrGene = df$StrgCorrGene[i],
WeakCorrGene = df$WeakCorrGene[i],
IC = df$IC[i])
rowdata <- rbind(rowdata, tmp)
}
#--------------------------------------------------
# Create a sign-by-sample matrix for variably correlated gene sets
#--------------------------------------------------
if(is.null(df$CountVariCorrGene[i])){
ssm_vari <- NA
}else{
if(df$CountVariCorrGene[i] == 0){
vector_vari <- matrix(0, ncol = dim(mat)[2], nrow = 1,
dimnames = list(NULL, colnames(mat)))
}else{
genes_vari <- unlist(strsplit(df$VariCorrGene[i], "/"))
submat_vari <- matrix(ncol = dim(mat)[2], nrow = 0,
dimnames = list(NULL, colnames(mat)))
inds <- which(rownames(mat) %in% genes_vari)
submat_vari <- rbind(submat_vari, mat[inds, ])
vector_vari <- apply(submat_vari, 2, mean)
}
ssm_vari <- matrix(ncol = dim(mat)[2], nrow = 0,
dimnames = list(NULL, colnames(mat)))
tmp <- weight_vari * vector_vari + (1.0 - weight_vari) * vector_weak
ssm_vari <- rbind(ssm_vari, tmp)
rownames(ssm_vari) <- paste(df$SignID[i], "-", "V", sep = "")
res <- rbind(res, ssm_vari)
tmp <- data.frame(ParentSignID = df$SignID[i],
Description = df$Description[i],
CorrGene = df$VariCorrGene[i],
WeakCorrGene = df$WeakCorrGene[i],
IC = df$IC[i])
rowdata <- rbind(rowdata, tmp)
}
}
}
}
new_sce <- SingleCellExperiment(assays = list(counts = res),
rowData = rowdata, colData = colData(sce))
for(k in seq_along(s_or_v)){
metadata(new_sce)[[s_or_v[k]]] <- metadata(sce)[[s_or_v[k]]]
}
if(!is.null(metadata(sce)[["sign_all"]])){
metadata(new_sce)[["sign_all"]] <- metadata(sce)[["sign_all"]]
}
if(length(altExpNames(sce)) != 0){
for(i in seq_along(altExpNames(sce))){
altExp(new_sce, altExpNames(sce)[i]) <- altExp(sce, altExpNames(sce)[i])
}
}
return(new_sce)
}
keita-iida/ASURATBI documentation built on Feb. 16, 2023, 9:37 a.m.
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Defines functions makeSignMatrix select_signs_manually remove_signs_manually remove_signs_redundant create_signs cluster_genesets remove_signs
Documented in cluster_genesets create_signs makeSignMatrix remove_signs remove_signs_manually remove_signs_redundant select_signs_manually
#-----------------------------------------------------------------------------80
#
#-----------------------------------------------------------------------------80
#' Remove signs including too few or too many genes.
#'
#' This function removes signs including too few or too many genes.
#'
#' @param sce A SingleCellExperiment object.
#' @param min_ngenes Minimum number of genes, which must be greater than one.
#' @param max_ngenes Maximum number of genes, which must be greater than one.
#'
#' @return A SingleCellExperiment object.
#' @import SingleCellExperiment
#' @import SummarizedExperiment
#' @import S4Vectors
#' @export
#'
#' @examples
#' data(pbmc_eg)
#' data(human_GO_eg)
#' pbmcs <- list(GO = pbmc_eg)
#' S4Vectors::metadata(pbmcs$GO) <- list(sign = human_GO_eg[["BP"]])
#' pbmcs$GO <- remove_signs(sce = pbmcs$GO, min_ngenes = 2, max_ngenes = 1000)
#' # The results are stored in `metadata(pbmcs$GO)$sign`.
#'
remove_signs <- function(sce = NULL, min_ngenes = 2, max_ngenes = 1000){
#--------------------------------------------------
# Error handling
#--------------------------------------------------
if(is.null(metadata(sce)$sign)){
stop("metadata(sce)$sign must have a database.")
}
if(min_ngenes <= 1){ stop("min_ngenes should be >= 2.") }
if(max_ngenes <= 1){ stop("max_ngenes should be >= 2.") }
#--------------------------------------------------
# Select innate genes.
#--------------------------------------------------
innate_g <- data.frame(gene = rownames(sce), geneID = rowData(sce)$geneID)
tmp <- metadata(sce)$sign
for(i in seq_len(nrow(tmp))){
#------------------------------
# GeneID: ENTREZ Gene ID
#------------------------------
geneIDs <- unlist(strsplit(tmp$GeneID[i], "/"))
geneIDs <- geneIDs[which(geneIDs %in% innate_g$geneID)]
tmp$GeneID[i] <- paste(geneIDs, collapse = "/")
#------------------------------
# Gene: gene symbol
#------------------------------
genes <- c()
for(j in seq_len(length(geneIDs))){
genes <- c(genes, innate_g[which(innate_g$geneID == geneIDs[j]), ]$gene)
}
tmp$Gene[i] <- paste(genes, collapse = "/")
#------------------------------
# Count
#------------------------------
tmp$Count[i] <- as.integer(length(geneIDs))
}
metadata(sce)$sign <- tmp
#--------------------------------------------------
# Remove IDs including too few or too many genes.
#--------------------------------------------------
tmp <- metadata(sce)$sign
res <- tmp[which((tmp$Count >= min_ngenes) & (tmp$Count <= max_ngenes)), ]
rownames(res) <- seq_len(nrow(res))
metadata(sce)$sign <- as.data.frame(res)
return(sce)
}
#-----------------------------------------------------------------------------80
#
#-----------------------------------------------------------------------------80
#' Cluster each functional gene set into three groups.
#'
#' This function clusters each functional gene set into strongly, variably, and
#' weakly correlated gene sets.
#'
#' @param sce A SingleCellExperiment object.
#' @param cormat A correlation matrix of gene expressions.
#' @param th_posi A threshold of positive correlation coefficient.
#' @param th_nega A threshold of negative correlation coefficient.
#'
#' @return A SingleCellExperiment object.
#' @import SingleCellExperiment
#' @import SummarizedExperiment
#' @import S4Vectors
#' @importFrom cluster pam
#' @export
#'
#' @examples
#' data(pbmc_eg)
#' data(human_GO_eg)
#' mat <- t(as.matrix(SummarizedExperiment::assay(pbmc_eg, "centered")))
#' pbmc_cormat <- cor(mat, method = "spearman")
#' pbmcs <- list(GO = pbmc_eg)
#' S4Vectors::metadata(pbmcs$GO) <- list(sign = human_GO_eg[["BP"]])
#' pbmcs$GO <- remove_signs(sce = pbmcs$GO, min_ngenes = 2, max_ngenes = 1000)
#' pbmcs$GO <- cluster_genesets(sce = pbmcs$GO, cormat = pbmc_cormat,
#' th_posi = 0.24, th_nega = -0.20)
#' # The results are stored in `metadata(pbmcs$GO)$sign`.
#'
cluster_genesets <- function(
sce = NULL, cormat = NULL, th_posi = NULL, th_nega = NULL
){
#--------------------------------------------------
# Error handling
#--------------------------------------------------
if(th_posi < 0){ stop("th_posi should be >= 0.") }
if(th_nega > 0){ stop("th_nega should be <= 0.") }
#--------------------------------------------------
# Correlation graph-based decomposition of FGSs
#--------------------------------------------------
df <- metadata(sce)$sign
res <- c("SignID", "Description", "IC",
"CountStrgCorrGene", "CountVariCorrGene", "CountWeakCorrGene",
"CorrStrg", "CorrVari", "CorrWeak",
"StrgCorrGene", "VariCorrGene", "WeakCorrGene",
"StrgCorrGeneID", "VariCorrGeneID", "WeakCorrGeneID")
res <- data.frame(matrix(ncol = 15, nrow = 0, dimnames = list(NULL, res)))
for(i in seq_len(nrow(df))){
genes <- unlist(strsplit(df$Gene[i], "/"))
if(length(genes) <= 1){
next
}
inds <- which(rownames(cormat) %in% genes)
if(length(inds) <= 2){
next
}
mat <- cormat[inds, inds]
#--------------------------------------------------
# Select genes having strong correlations with others.
#--------------------------------------------------
diag(mat) <- -99
inds_posi <- which(apply(mat, 2, function(x) sum(x >= th_posi)) > 0)
diag(mat) <- 99
inds_nega <- which(apply(mat, 2, function(x) sum(x <= th_nega)) > 0)
if(length(inds_posi) == 0){
#--------------------------------------------------
# Define strongly, variably, and weakly correlated gene sets.
#--------------------------------------------------
genes_strg <- NA ; genes_vari <- NA ; genes_weak <- genes
mean_strg <- NA ; mean_vari <- NA
mean_weak <- ifelse(length(genes_weak) <= 1, NA, mean(mat[mat <= 1]))
}else{
if(length(inds_nega) == 0){
#--------------------------------------------------
# Define strongly, variably, and weakly correlated gene sets.
#--------------------------------------------------
genes_vari <- NA ; mean_vari <- NA
submat <- mat[inds_posi, inds_posi]
genes_strg <- rownames(submat)
mean_strg <- ifelse(length(genes_strg) <= 1, NA,
mean(submat[submat <= 1]))
if(mean_strg < th_posi){
genes_strg <- NA ; mean_strg <- NA
genes_weak <- genes
mean_weak <- ifelse(length(genes_weak) <= 1, NA, mean(mat[mat <= 1]))
}else{
genes_weak <- setdiff(genes, genes_strg)
inds <- which(rownames(mat) %in% genes_weak)
tmp <- mat[inds, inds]
mean_weak <- ifelse(length(inds) <= 1, NA, mean(tmp[tmp <= 1]))
}
}else{
inds <- union(inds_posi, inds_nega)
submat <- mat[inds, inds] ; diag(submat) <- 1
#--------------------------------------------------
# PAM clustering using cluster package
#--------------------------------------------------
c <- pam(submat, k = 2)
diag(submat) <- 99
gset <- list() ; mu <- c()
for(j in seq_len(2)){
gset[[j]] <- names(c[["clustering"]])[which(c[["clustering"]] == j)]
inds <- which(rownames(submat) %in% gset[[j]])
tmp <- submat[inds, inds]
mu[j] <- ifelse(length(inds) <= 1, NA, mean(tmp[tmp <= 1]))
}
#--------------------------------------------------
# Define strongly, variably, and weakly correlated gene sets.
#--------------------------------------------------
inds <- order(mu, decreasing = TRUE)
genes_strg <- gset[[inds[1]]]
mean_strg <- mu[inds[1]]
if(mean_strg < th_posi){
genes_strg <- NA ; mean_strg <- NA
genes_vari <- NA ; mean_vari <- NA
genes_weak <- genes
mean_weak <- ifelse(length(genes_weak) <= 1, NA, mean(mat[mat <= 1]))
}else{
genes_vari <- gset[[inds[2]]]
mean_vari <- mu[inds[2]]
genes_weak <- setdiff(genes, union(gset[[1]], gset[[2]]))
inds <- which(rownames(mat) %in% genes_weak)
tmp <- mat[inds, inds]
mean_weak <- ifelse(length(inds) <= 1, NA, mean(tmp[tmp <= 1]))
}
}
}
#--------------------------------------------------
# Result
#--------------------------------------------------
tmp <- as.data.frame(rowData(sce))
if(is.element(NA, genes_strg)){
genes_strg <- NA ; geneIDs_strg <- NA ; count_strg <- 0
}else{
count_strg <- length(genes_strg)
gs <- c()
for(j in seq_along(genes_strg)){
inds <- which(rownames(tmp) == genes_strg[j])
if(ncol(tmp) == 1){
if(colnames(tmp) == "geneID"){
gs <- c(gs, tmp[inds, ])
}else{
stop("rowData() has only one column; the name must be \"geneID\".")
}
}else{
gs <- c(gs, tmp[inds, ]$geneID)
}
}
geneIDs_strg <- paste(gs, collapse = "/")
genes_strg <- paste(genes_strg, collapse = "/")
}
if(is.element(NA, genes_vari)){
genes_vari <- NA ; geneIDs_vari <- NA ; count_vari <- 0
}else{
count_vari <- length(genes_vari)
gs <- c()
for(j in seq_along(genes_vari)){
inds <- which(rownames(tmp) == genes_vari[j])
if(ncol(tmp) == 1){
if(colnames(tmp) == "geneID"){
gs <- c(gs, tmp[inds, ])
}else{
stop("rowData() has only one column; the name must be \"geneID\".")
}
}else{
gs <- c(gs, tmp[inds, ]$geneID)
}
}
geneIDs_vari <- paste(gs, collapse = "/")
genes_vari <- paste(genes_vari, collapse = "/")
}
if(is.element(NA, genes_weak)){
genes_weak <- NA ; geneIDs_weak <- NA ; count_weak <- 0
}else{
count_weak <- length(genes_weak)
gs <- c()
for(j in seq_along(genes_weak)){
inds <- which(rownames(tmp) == genes_weak[j])
if(ncol(tmp) == 1){
if(colnames(tmp) == "geneID"){
gs <- c(gs, tmp[inds, ])
}else{
stop("rowData() has only one column; the name must be \"geneID\".")
}
}else{
gs <- c(gs, tmp[inds, ]$geneID)
}
}
geneIDs_weak <- paste(gs, collapse = "/")
genes_weak <- paste(genes_weak, collapse = "/")
}
dg <- data.frame(SignID = df$ID[i], Description = df$Description[i],
IC = df$IC[i],
CountStrgCorrGene = count_strg,
CountVariCorrGene = count_vari,
CountWeakCorrGene = count_weak,
CorrStrg = mean_strg,
CorrVari = mean_vari,
CorrWeak = mean_weak,
StrgCorrGene = genes_strg,
VariCorrGene = genes_vari,
WeakCorrGene = genes_weak,
StrgCorrGeneID = geneIDs_strg,
VariCorrGeneID = geneIDs_vari,
WeakCorrGeneID = geneIDs_weak)
res <- rbind(res, dg)
}
metadata(sce)$sign <- res
return(sce)
}
#-----------------------------------------------------------------------------80
#
#-----------------------------------------------------------------------------80
#' Define signs for strongly and variably correlated gene sets.
#'
#' This function define signs for strongly and variably correlated gene sets.
#'
#' @param sce A SingleCellExperiment object.
#' @param min_cnt_strg An integer for the cutoff value for strongly correlated
#' gene sets.
#' @param min_cnt_vari An integer for the cutoff value for variably correlated
#' gene sets.
#'
#' @return A SingleCellExperiment object.
#' @import SingleCellExperiment
#' @import SummarizedExperiment
#' @import S4Vectors
#' @export
#'
#' @examples
#' data(pbmc_eg)
#' data(human_GO_eg)
#' mat <- t(as.matrix(SummarizedExperiment::assay(pbmc_eg, "centered")))
#' pbmc_cormat <- cor(mat, method = "spearman")
#' pbmcs <- list(GO = pbmc_eg)
#' S4Vectors::metadata(pbmcs$GO) <- list(sign = human_GO_eg[["BP"]])
#' pbmcs$GO <- remove_signs(sce = pbmcs$GO, min_ngenes = 2, max_ngenes = 1000)
#' pbmcs$GO <- cluster_genesets(sce = pbmcs$GO, cormat = pbmc_cormat,
#' th_posi = 0.24, th_nega = -0.20)
#' pbmcs$GO <- create_signs(sce = pbmcs$GO, min_cnt_strg = 2, min_cnt_vari = 2)
#' # The results are stored in `metadata(pbmcs$GO)$sign_all`.
#'
create_signs <- function(sce = NULL, min_cnt_strg = 2, min_cnt_vari = 2){
#--------------------------------------------------
# Error handling
#--------------------------------------------------
if(min_cnt_strg <= 0){ stop("min_cnt_strg should be >= 1.") }
if(min_cnt_vari <= 0){ stop("min_cnt_vari should be >= 1.") }
df <- metadata(sce)$sign
#--------------------------------------------------
# Strongly correlated gene sets
#--------------------------------------------------
df_strg <- df[which(df$CountStrgCorrGene >= min_cnt_strg), ]
if(nrow(df_strg) >= 1){
df_strg <- data.frame(
SignID = df_strg$SignID, Description = df_strg$Description,
IC = df_strg$IC,
CountStrgCorrGene = df_strg$CountStrgCorrGene,
CountWeakCorrGene = df_strg$CountWeakCorrGene,
CorrStrg = df_strg$CorrStrg, CorrWeak = df_strg$CorrWeak,
StrgCorrGene = df_strg$StrgCorrGene, WeakCorrGene = df_strg$WeakCorrGene,
StrgCorrGeneID = df_strg$StrgCorrGeneID,
WeakCorrGeneID = df_strg$WeakCorrGeneID)
}
#--------------------------------------------------
# Variably correlated gene sets
#--------------------------------------------------
df_vari <- df[which(df$CountVariCorrGene >= min_cnt_vari), ]
if(nrow(df_vari) >= 1){
df_vari <- data.frame(
SignID = df_vari$SignID, Description = df_vari$Description,
IC = df_vari$IC,
CountVariCorrGene = df_vari$CountVariCorrGene,
CountWeakCorrGene = df_vari$CountWeakCorrGene,
CorrVari = df_vari$CorrVari, CorrWeak = df_vari$CorrWeak,
VariCorrGene = df_vari$VariCorrGene, WeakCorrGene = df_vari$WeakCorrGene,
VariCorrGeneID = df_vari$VariCorrGeneID,
WeakCorrGeneID = df_vari$WeakCorrGeneID)
}
#--------------------------------------------------
# Store the results.
#--------------------------------------------------
metadata(sce)$sign_SCG <- df_strg
metadata(sce)$sign_VCG <- df_vari
#--------------------------------------------------
# Add metadata(sce)$sign_all.
#--------------------------------------------------
metadata(sce)$sign <- NULL
tmp <- c("SignID", "Description", "IC",
"CountCorrGene", "CountWeakCorrGene", "Corr", "CorrWeak",
"CorrGene", "WeakCorrGene", "CorrGeneID", "WeakCorrGeneID")
colnames(df_strg) <- tmp
colnames(df_vari) <- tmp
if(nrow(df_strg) == 0){
stop("SCG is not defined.")
}else{
if(nrow(df_vari) == 0){
metadata(sce)$sign_all <- cbind(CorrType = "SCG", df_strg)
}else{
metadata(sce)$sign_all <- rbind(cbind(CorrType = "SCG", df_strg),
cbind(CorrType = "VCG", df_vari))
}
}
return(sce)
}
#-----------------------------------------------------------------------------80
#
#-----------------------------------------------------------------------------80
#' Remove redundant signs using semantic similarity matrices.
#'
#' This function removes redundant signs using semantic similarity matrices.
#'
#' @param sce A SingleCellExperiment object.
#' @param similarity_matrix A semantic similarity matrix.
#' @param threshold A threshold value of semantic similarity, used for
#' regarding biological terms as similar ones
#' @param keep_rareID If TRUE, biological terms with the larger ICs are kept.
#'
#' @return A SingleCellExperiment object.
#' @import SingleCellExperiment
#' @import SummarizedExperiment
#' @import S4Vectors
#' @export
#'
#' @examples
#' data(pbmc_eg)
#' data(human_GO_eg)
#' mat <- t(as.matrix(SummarizedExperiment::assay(pbmc_eg, "centered")))
#' pbmc_cormat <- cor(mat, method = "spearman")
#' pbmcs <- list(GO = pbmc_eg)
#' S4Vectors::metadata(pbmcs$GO) <- list(sign = human_GO_eg[["BP"]])
#' pbmcs$GO <- remove_signs(sce = pbmcs$GO, min_ngenes = 2, max_ngenes = 1000)
#' pbmcs$GO <- cluster_genesets(sce = pbmcs$GO, cormat = pbmc_cormat,
#' th_posi = 0.24, th_nega = -0.20)
#' pbmcs$GO <- create_signs(sce = pbmcs$GO, min_cnt_strg = 2, min_cnt_vari = 2)
#' pbmcs$GO <- remove_signs_redundant(
#' sce = pbmcs$GO, similarity_matrix = human_GO_eg$similarity_matrix$BP,
#' threshold = 0.80, keep_rareID = TRUE)
#' # The results are stored in `metadata(pbmcs$GO)$sign_SCG`,
#' # `metadata(pbmcs$GO)$sign_VCG`, `metadata(pbmcs$GO)$sign_all`,
#' # and if there exist, `metadata(pbmcs$GO)$sign_SCG_redundant` and
#' # `metadata(pbmcs$GO)$sign_VCG_redundant`.
#'
remove_signs_redundant <- function(
sce = NULL, similarity_matrix = NULL, threshold = NULL, keep_rareID = NULL
){
#--------------------------------------------------
# Error handling
#--------------------------------------------------
if(is.null(similarity_matrix)){
stop("Semantic similarity is not defined. Skip this process.")
}
report <- list()
s_or_v <- c("sign_SCG", "sign_VCG")
for(k in seq_along(s_or_v)){
#--------------------------------------------------
# Report format
#--------------------------------------------------
df <- metadata(sce)[[s_or_v[k]]]
df <- df[!(is.na(df$IC)), ]
if(nrow(df) == 0){
next
}
inds <- which(rownames(similarity_matrix) %in% df$SignID)
if(length(inds) < 2){
next
}
submat <- similarity_matrix[inds, inds]
inds <- order(df$IC, decreasing = FALSE)
submat <- submat[inds, inds]
report[[k]] <- c("Similarity", "Kept_SignID", "Removed_SignID",
"Kept_Description", "Removed_Description",
"Kept_GeneCount", "Removed_GeneCount",
"Kept_Gene", "Removed_Gene", "Kept_IC", "Removed_IC")
report[[k]] <- data.frame(matrix(ncol = 11, nrow = 0,
dimnames = list(NULL, report[[k]])))
flag <- rep(0, dim(submat)[1])
if(keep_rareID == TRUE){
#--------------------------------------------------
# case I
#--------------------------------------------------
I <- dim(submat)[1]
for(i in seq(I, 2)){
J <- dim(submat)[2] - (I - i + 1) # Be careful
if(flag[i] == 1){ # Be careful
next
}
for(j in seq_len(J)){
if(is.na(submat[i, j])){
next
}
if(abs(submat[i, j]) >= threshold){
ind_kept <- which(df$SignID == rownames(submat)[i])
ind_remo <- which(df$SignID == rownames(submat)[j])
if(k == 1){
kept_count <- df[ind_kept, ]$CountStrgCorrGene +
df[ind_kept, ]$CountWeakCorrGene
remo_count <- df[ind_remo, ]$CountStrgCorrGene +
df[ind_remo, ]$CountWeakCorrGene
kept_genes <- paste(df[ind_kept, ]$StrgCorrGene,
df[ind_kept, ]$WeakCorrGene, sep = "/")
remo_genes <- paste(df[ind_remo, ]$StrgCorrGene,
df[ind_remo, ]$WeakCorrGene, sep = "/")
}else if(k == 2){
kept_count <- df[ind_kept, ]$CountVariCorrGene +
df[ind_kept, ]$CountWeakCorrGene
remo_count <- df[ind_remo, ]$CountVariCorrGene +
df[ind_remo, ]$CountWeakCorrGene
kept_genes <- paste(df[ind_kept, ]$VariCorrGene,
df[ind_kept, ]$WeakCorrGene, sep = "/")
remo_genes <- paste(df[ind_remo, ]$VariCorrGene,
df[ind_remo, ]$WeakCorrGene, sep = "/")
}
report[[k]] <- rbind(report[[k]], data.frame(
Similarity = submat[i, j],
Kept_SignID = df[ind_kept, ]$SignID,
Removed_SignID = df[ind_remo, ]$SignID,
Kept_Description = df[ind_kept, ]$Description,
Removed_Description = df[ind_remo, ]$Description,
Kept_GeneCount = kept_count,
Removed_GeneCount = remo_count,
Kept_Gene = kept_genes,
Removed_Gene = remo_genes,
Kept_IC = df[ind_kept, ]$IC,
Removed_IC = df[ind_remo, ]$IC
))
flag[j] <- 1
}
}
}
}else{
#--------------------------------------------------
# case II
#--------------------------------------------------
I <- dim(submat)[1] - 1
J <- dim(submat)[2]
for(i in seq_len(I)){
j0 <- i + 1 # Be careful
if(flag[i] == 1){ # Be careful
next
}
for(j in seq(j0, J)){
if(is.na(submat[i, j])){
next
}
if(abs(submat[i, j]) >= threshold){
ind_kept <- which(df$SignID == rownames(submat)[i])
ind_remo <- which(df$SignID == rownames(submat)[j])
if(k == 1){
kept_count <- df[ind_kept, ]$CountStrgCorrGene +
df[ind_kept, ]$CountWeakCorrGene
remo_count <- df[ind_remo, ]$CountStrgCorrGene +
df[ind_remo, ]$CountWeakCorrGene
kept_genes <- paste(df[ind_kept, ]$StrgCorrGene,
df[ind_kept, ]$WeakCorrGene, sep = "/")
remo_genes <- paste(df[ind_remo, ]$StrgCorrGene,
df[ind_remo, ]$WeakCorrGene, sep = "/")
}else if(k == 2){
kept_count <- df[ind_kept, ]$CountVariCorrGene +
df[ind_kept, ]$CountWeakCorrGene
remo_count <- df[ind_remo, ]$CountVariCorrGene +
df[ind_remo, ]$CountWeakCorrGene
kept_genes <- paste(df[ind_kept, ]$VariCorrGene,
df[ind_kept, ]$WeakCorrGene, sep = "/")
remo_genes <- paste(df[ind_remo, ]$VariCorrGene,
df[ind_remo, ]$WeakCorrGene, sep = "/")
}
report[[k]] <- rbind(report[[k]], data.frame(
Similarity = submat[i, j],
Kept_SignID = df[ind_kept, ]$SignID,
Removed_SignID = df[ind_remo, ]$SignID,
Kept_Description = df[ind_kept, ]$Description,
Removed_Description = df[ind_remo, ]$Description,
Kept_GeneCount = kept_count,
Removed_GeneCount = remo_count,
Kept_Gene = kept_genes,
Removed_Gene = remo_genes,
Kept_IC = df[ind_kept, ]$IC,
Removed_IC = df[ind_remo, ]$IC
))
flag[j] <- 1
}
}
}
}
#--------------------------------------------------
# Remove redundant signs.
#--------------------------------------------------
if(length(report[[k]]$Removed_SignID) >= 1){
kept_IDs <- setdiff(df$SignID, report[[k]]$Removed_SignID)
res <- df[which(df$SignID %in% kept_IDs), ]
rownames(res) <- seq_len(nrow(res))
}else{
res <- df
}
metadata(sce)[[s_or_v[k]]] <- res
}
#--------------------------------------------------
# Modify metadata(sce)$sign_all.
#--------------------------------------------------
df_strg <- as.data.frame(metadata(sce)$sign_SCG)
df_vari <- as.data.frame(metadata(sce)$sign_VCG)
tmp <- c("SignID", "Description", "IC",
"CountCorrGene", "CountWeakCorrGene", "Corr", "CorrWeak",
"CorrGene", "WeakCorrGene", "CorrGeneID", "WeakCorrGeneID")
colnames(df_strg) <- tmp
colnames(df_vari) <- tmp
if(nrow(df_strg) == 0){
stop("SCG is not defined.")
}else{
if(nrow(df_vari) == 0){
metadata(sce)$sign_all <- cbind(CorrType = "SCG", df_strg)
}else{
metadata(sce)$sign_all <- rbind(cbind(CorrType = "SCG", df_strg),
cbind(CorrType = "VCG", df_vari))
}
}
#--------------------------------------------------
# Store the report.
#--------------------------------------------------
for(k in seq_along(s_or_v)){
if(nrow(metadata(sce)[[s_or_v[k]]]) < 2){
next
}
text <- paste(s_or_v[k], "redundant", sep = "_")
metadata(sce)[[text]] <- report[[k]]
}
return(sce)
}
#-----------------------------------------------------------------------------80
#
#-----------------------------------------------------------------------------80
#' Remove signs by specifying keywords.
#'
#' This function removes signs by specifying keywords.
#'
#' @param sce A SingleCellExperiment object.
#' @param keywords keywords separated by pipes `|`.
#'
#' @return A SingleCellExperiment object.
#' @import SingleCellExperiment
#' @import SummarizedExperiment
#' @import S4Vectors
#' @export
#'
#' @examples
#' data(pbmc_eg)
#' data(human_GO_eg)
#' mat <- t(as.matrix(SummarizedExperiment::assay(pbmc_eg, "centered")))
#' pbmc_cormat <- cor(mat, method = "spearman")
#' pbmcs <- list(GO = pbmc_eg)
#' S4Vectors::metadata(pbmcs$GO) <- list(sign = human_GO_eg[["BP"]])
#' pbmcs$GO <- remove_signs(sce = pbmcs$GO, min_ngenes = 2, max_ngenes = 1000)
#' pbmcs$GO <- cluster_genesets(sce = pbmcs$GO, cormat = pbmc_cormat,
#' th_posi = 0.24, th_nega = -0.20)
#' pbmcs$GO <- create_signs(sce = pbmcs$GO, min_cnt_strg = 2, min_cnt_vari = 2)
#' keywords <- "Covid19|foofoo|hogehoge"
#' pbmcs$GO <- remove_signs_manually(sce = pbmcs$GO, keywords = keywords)
#' # The results are stored in `metadata(pbmcs$GO)$sign_SCG`,
#' # `metadata(pbmcs$GO)$sign_VCG`, and `metadata(pbmcs$GO)$sign_all`.
#'
remove_signs_manually <- function(sce = NULL, keywords = NULL){
if(is.null(keywords)){
return(sce)
}
s_or_v <- c("sign_SCG", "sign_VCG")
for(k in seq_along(s_or_v)){
df <- metadata(sce)[[s_or_v[k]]]
if(nrow(df) != 0){
tmp <- ((grepl(keywords, df$SignID)) | (grepl(keywords, df$Description)))
df <- df[!tmp, ]
rownames(df) <- seq_len(nrow(df))
}
metadata(sce)[[s_or_v[k]]] <- df
}
#--------------------------------------------------
# Modify metadata(sce)$sign_all.
#--------------------------------------------------
df_strg <- as.data.frame(metadata(sce)$sign_SCG)
df_vari <- as.data.frame(metadata(sce)$sign_VCG)
tmp <- c("SignID", "Description", "IC",
"CountCorrGene", "CountWeakCorrGene", "Corr", "CorrWeak",
"CorrGene", "WeakCorrGene", "CorrGeneID", "WeakCorrGeneID")
colnames(df_strg) <- tmp
colnames(df_vari) <- tmp
if(nrow(df_strg) == 0){
stop("SCG is not defined.")
}else{
if(nrow(df_vari) == 0){
metadata(sce)$sign_all <- cbind(CorrType = "SCG", df_strg)
}else{
metadata(sce)$sign_all <- rbind(cbind(CorrType = "SCG", df_strg),
cbind(CorrType = "VCG", df_vari))
}
}
return(sce)
}
#-----------------------------------------------------------------------------80
#
#-----------------------------------------------------------------------------80
#' Select signs by specifying keywords.
#'
#' This function selects signs by specifying keywords.
#'
#' @param sce An ASURAT object.
#' @param keywords Keywords separated by a pipe.
#'
#' @return An ASURAT object.
#' @import SingleCellExperiment
#' @import SummarizedExperiment
#' @import S4Vectors
#' @export
#'
#' @examples
#' data(pbmc_eg)
#' data(human_GO_eg)
#' mat <- t(as.matrix(SummarizedExperiment::assay(pbmc_eg, "centered")))
#' pbmc_cormat <- cor(mat, method = "spearman")
#' pbmcs <- list(GO = pbmc_eg)
#' S4Vectors::metadata(pbmcs$GO) <- list(sign = human_GO_eg[["BP"]])
#' pbmcs$GO <- remove_signs(sce = pbmcs$GO, min_ngenes = 2, max_ngenes = 1000)
#' pbmcs$GO <- cluster_genesets(sce = pbmcs$GO, cormat = pbmc_cormat,
#' th_posi = 0.24, th_nega = -0.20)
#' pbmcs$GO <- create_signs(sce = pbmcs$GO, min_cnt_strg = 2, min_cnt_vari = 2)
#' keywords <- "cell|process"
#' pbmcs$GO <- select_signs_manually(sce = pbmcs$GO, keywords = keywords)
#' # The results are stored in `metadata(pbmcs$GO)$sign_SCG`,
#' # `metadata(pbmcs$GO)$sign_VCG`, and `metadata(pbmcs$GO)$sign_all`.
#'
select_signs_manually <- function(sce = NULL, keywords = NULL){
if(is.null(keywords)){
return(sce)
}
s_or_v <- c("sign_SCG", "sign_VCG")
for(k in seq_along(s_or_v)){
df <- metadata(sce)[[s_or_v[k]]]
if(nrow(df) != 0){
tmp <- ((grepl(keywords, df$SignID)) | (grepl(keywords, df$Description)))
df <- df[tmp, ]
rownames(df) <- seq_len(nrow(df))
}
metadata(sce)[[s_or_v[k]]] <- df
}
#--------------------------------------------------
# Modify metadata(sce)$sign_all.
#--------------------------------------------------
df_strg <- as.data.frame(metadata(sce)$sign_SCG)
df_vari <- as.data.frame(metadata(sce)$sign_VCG)
tmp <- c("SignID", "Description", "IC",
"CountCorrGene", "CountWeakCorrGene", "Corr", "CorrWeak",
"CorrGene", "WeakCorrGene", "CorrGeneID", "WeakCorrGeneID")
colnames(df_strg) <- tmp
colnames(df_vari) <- tmp
if(nrow(df_strg) == 0){
stop("SCG is not defined. The keywords may not be included in the data.")
}else{
if(nrow(df_vari) == 0){
metadata(sce)$sign_all <- cbind(CorrType = "SCG", df_strg)
}else{
metadata(sce)$sign_all <- rbind(cbind(CorrType = "SCG", df_strg),
cbind(CorrType = "VCG", df_vari))
}
}
return(sce)
}
#-----------------------------------------------------------------------------80
#
#-----------------------------------------------------------------------------80
#' Create a new SingleCellExperiment object for sign-by-sample matrices.
#'
#' This function creates a new SingleCellExperiment object for sign-by-sample
#' matrices (SSM) by concatenating SSMs for strongly and variably correlated
#' gene sets.
#'
#' @param sce A SingleCellExperiment object.
#' @param weight_strg A weight parameter for strongly correlated gene sets.
#' @param weight_vari A weight parameter for variably correlated gene sets.
#'
#' @return A SingleCellExperiment object.
#' @import SingleCellExperiment
#' @import SummarizedExperiment
#' @import S4Vectors
#' @export
#'
#' @examples
#' data(pbmc_eg)
#' data(human_GO_eg)
#' mat <- t(as.matrix(SummarizedExperiment::assay(pbmc_eg, "centered")))
#' pbmc_cormat <- cor(mat, method = "spearman")
#' pbmcs <- list(GO = pbmc_eg)
#' S4Vectors::metadata(pbmcs$GO) <- list(sign = human_GO_eg[["BP"]])
#' pbmcs$GO <- remove_signs(sce = pbmcs$GO, min_ngenes = 2, max_ngenes = 1000)
#' pbmcs$GO <- cluster_genesets(sce = pbmcs$GO, cormat = pbmc_cormat,
#' th_posi = 0.24, th_nega = -0.20)
#' pbmcs$GO <- create_signs(sce = pbmcs$GO, min_cnt_strg = 2, min_cnt_vari = 2)
#' pbmcs$GO <- makeSignMatrix(sce = pbmcs$GO, weight_strg = 0.5,
#' weight_vari = 0.5)
#' # The resutls can be check by, e.g., assay(pbmcs$GO, "counts").
#'
makeSignMatrix <- function(sce = NULL, weight_strg = 0.5, weight_vari = 0.5){
#--------------------------------------------------
# Error handling
#--------------------------------------------------
if((weight_strg == 99) & (weight_strg == 99)){
message("Search a way to bring harmony.")
}
if((weight_strg < 0) | (weight_strg > 1) |
(weight_vari < 0) | (weight_vari > 1)){
stop("weight_* must be values in [0, 1].")
}
mat <- assay(sce, "centered")
res <- matrix(ncol = dim(mat)[2], nrow = 0,
dimnames = list(NULL, colnames(mat)))
rowdata <- c("ParentSignID", "Description", "CorrGene", "WeakCorrGene", "IC")
rowdata <- matrix(ncol = 5, nrow = 0, dimnames = list(NULL, rowdata))
s_or_v <- c("sign_SCG", "sign_VCG")
for(k in seq_along(s_or_v)){
df <- metadata(sce)[[s_or_v[k]]]
if(nrow(df) != 0){
for(i in seq_len(nrow(df))){
#--------------------------------------------------
# Create a sign-by-sample matrix for weakly correlated gene sets
#--------------------------------------------------
if(df$CountWeakCorrGene[i] == 0){
vector_weak <- matrix(0, ncol = dim(mat)[2], nrow = 1,
dimnames = list(NULL, colnames(mat)))
}else{
genes_weak <- unlist(strsplit(df$WeakCorrGene[i], "/"))
submat_weak <- matrix(ncol = dim(mat)[2], nrow = 0,
dimnames = list(NULL, colnames(mat)))
inds <- which(rownames(mat) %in% genes_weak)
submat_weak <- rbind(submat_weak, mat[inds, ])
vector_weak <- apply(submat_weak, 2, mean)
}
#--------------------------------------------------
# Create a sign-by-sample matrix for strongly correlated gene sets
#--------------------------------------------------
if(is.null(df$CountStrgCorrGene[i])){
ssm_strg <- NA
}else{
if(df$CountStrgCorrGene[i] == 0){
vector_strg <- matrix(0, ncol = dim(mat)[2], nrow = 1,
dimnames = list(NULL, colnames(mat)))
}else{
genes_strg <- unlist(strsplit(df$StrgCorrGene[i], "/"))
submat_strg <- matrix(ncol = dim(mat)[2], nrow = 0,
dimnames = list(NULL, colnames(mat)))
inds <- which(rownames(mat) %in% genes_strg)
submat_strg <- rbind(submat_strg, mat[inds, ])
vector_strg <- apply(submat_strg, 2, mean)
}
ssm_strg <- matrix(ncol = dim(mat)[2], nrow = 0,
dimnames = list(NULL, colnames(mat)))
tmp <- weight_strg * vector_strg + (1.0 - weight_strg) * vector_weak
ssm_strg <- rbind(ssm_strg, tmp)
rownames(ssm_strg) <- paste(df$SignID[i], "-", "S", sep = "")
res <- rbind(res, ssm_strg)
tmp <- data.frame(ParentSignID = df$SignID[i],
Description = df$Description[i],
CorrGene = df$StrgCorrGene[i],
WeakCorrGene = df$WeakCorrGene[i],
IC = df$IC[i])
rowdata <- rbind(rowdata, tmp)
}
#--------------------------------------------------
# Create a sign-by-sample matrix for variably correlated gene sets
#--------------------------------------------------
if(is.null(df$CountVariCorrGene[i])){
ssm_vari <- NA
}else{
if(df$CountVariCorrGene[i] == 0){
vector_vari <- matrix(0, ncol = dim(mat)[2], nrow = 1,
dimnames = list(NULL, colnames(mat)))
}else{
genes_vari <- unlist(strsplit(df$VariCorrGene[i], "/"))
submat_vari <- matrix(ncol = dim(mat)[2], nrow = 0,
dimnames = list(NULL, colnames(mat)))
inds <- which(rownames(mat) %in% genes_vari)
submat_vari <- rbind(submat_vari, mat[inds, ])
vector_vari <- apply(submat_vari, 2, mean)
}
ssm_vari <- matrix(ncol = dim(mat)[2], nrow = 0,
dimnames = list(NULL, colnames(mat)))
tmp <- weight_vari * vector_vari + (1.0 - weight_vari) * vector_weak
ssm_vari <- rbind(ssm_vari, tmp)
rownames(ssm_vari) <- paste(df$SignID[i], "-", "V", sep = "")
res <- rbind(res, ssm_vari)
tmp <- data.frame(ParentSignID = df$SignID[i],
Description = df$Description[i],
CorrGene = df$VariCorrGene[i],
WeakCorrGene = df$WeakCorrGene[i],
IC = df$IC[i])
rowdata <- rbind(rowdata, tmp)
}
}
}
}
new_sce <- SingleCellExperiment(assays = list(counts = res),
rowData = rowdata, colData = colData(sce))
for(k in seq_along(s_or_v)){
metadata(new_sce)[[s_or_v[k]]] <- metadata(sce)[[s_or_v[k]]]
}
if(!is.null(metadata(sce)[["sign_all"]])){
metadata(new_sce)[["sign_all"]] <- metadata(sce)[["sign_all"]]
}
if(length(altExpNames(sce)) != 0){
for(i in seq_along(altExpNames(sce))){
altExp(new_sce, altExpNames(sce)[i]) <- altExp(sce, altExpNames(sce)[i])
}
}
return(new_sce)
}
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