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update tutorial #85

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update tutorial #85

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36c53cb
update tutorital
zktuong Oct 31, 2023
b832464
ok found the actual bug
zktuong Nov 1, 2023
8160f96
Update plot_cpdb.R
zktuong Nov 1, 2023
eaf44ad
Update utils.R
zktuong Nov 1, 2023
2d77290
Update utils.R
zktuong Nov 1, 2023
03fc888
Update plot_cpdb.R
zktuong Nov 1, 2023
eb5c72f
Update plot_cpdb.Rd
zktuong Nov 1, 2023
fae2dbd
hmm
zktuong Nov 1, 2023
a1544b6
revert to original behaviour
zktuong Nov 1, 2023
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606 changes: 387 additions & 219 deletions R/plot_cpdb.R
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55 changes: 36 additions & 19 deletions R/utils.R
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,22 @@ DEFAULT_V5_COL_START <- 14
DEFAULT_CLASS_COL <- 13
DEFAULT_COL_START <- 12

.prep_dimensions <- function(input, reference) {
requireNamespace("reshape2")
tmp_mat <- reference
tmp_mat <- (tmp_mat * 0) + 1
melted_A <- reshape2::melt(as.matrix(tmp_mat))
melted_B <- reshape2::melt(as.matrix(input))
rownames(melted_A) <- paste0(melted_A$Var1, DEFAULT_SEP, melted_A$Var2)
rownames(melted_B) <- paste0(melted_B$Var1, DEFAULT_SEP, melted_B$Var2)
melted_A[row.names(melted_B), ] <- melted_B
tmp_mat <- reshape2::dcast(melted_A, Var1 ~ Var2, value.var = "value")
rownames(tmp_mat) <- tmp_mat$Var1
tmp_mat <- tmp_mat[, -1]
tmp_mat <- tmp_mat[rownames(reference), colnames(reference)]
return(tmp_mat)
}


.prep_table <- function(data) {
dat <- data
Expand Down Expand Up @@ -36,18 +52,18 @@ DEFAULT_COL_START <- 12
.prep_query_group <- function(data, genes = NULL, gene_family = NULL, custom_gene_family = NULL) {
if (is.null(gene_family) & is.null(genes)) {
query_group <- NULL
query_id <- grep("", data$interacting_pair)
query <- row.names(data)[query_id]
query_id <- grep("", data$interacting_pair, value = TRUE)
query <- row.names(data[data$interacting_pair %in% query_id, ])
} else if (!is.null(gene_family) & !is.null(genes)) {
stop("Please specify either genes or gene_family, not both")
} else if (!is.null(gene_family) & is.null(genes)) {
chemokines <- grep("^CXC|CCL|CCR|CX3|XCL|XCR", data$interacting_pair)
th1 <- grep("IL2|IL12|IL18|IL27|IFNG|IL10|TNF$|TNF |LTA|LTB|STAT1|CCR5|CXCR3|IL12RB1|IFNGR1|TBX21|STAT4", data$interacting_pair)
th2 <- grep("IL4|IL5|IL25|IL10|IL13|AREG|STAT6|GATA3|IL4R", data$interacting_pair)
th17 <- grep("IL21|IL22|IL24|IL26|IL17A|IL17A|IL17F|IL17RA|IL10|RORC|RORA|STAT3|CCR4|CCR6|IL23RA|TGFB", data$interacting_pair)
treg <- grep("IL35|IL10|FOXP3|IL2RA|TGFB", data$interacting_pair)
costimulatory <- grep("CD86|CD80|CD48|LILRB2|LILRB4|TNF|CD2|ICAM|SLAM|LT[AB]|NECTIN2|CD40|CD70|CD27|CD28|CD58|TSLP|PVR|CD44|CD55|CD[1-9]", data$interacting_pair)
coinhibitory <- grep("SIRP|CD47|ICOS|TIGIT|CTLA4|PDCD1|CD274|LAG3|HAVCR|VSIR", data$interacting_pair)
chemokines <- grep("^CXC|CCL|CCR|CX3|XCL|XCR", data$interacting_pair, value = TRUE)
th1 <- grep("IL2|IL12|IL18|IL27|IFNG|IL10|TNF$|TNF |LTA|LTB|STAT1|CCR5|CXCR3|IL12RB1|IFNGR1|TBX21|STAT4", data$interacting_pair, value = TRUE)
th2 <- grep("IL4|IL5|IL25|IL10|IL13|AREG|STAT6|GATA3|IL4R", data$interacting_pair, value = TRUE)
th17 <- grep("IL21|IL22|IL24|IL26|IL17A|IL17A|IL17F|IL17RA|IL10|RORC|RORA|STAT3|CCR4|CCR6|IL23RA|TGFB", data$interacting_pair, value = TRUE)
treg <- grep("IL35|IL10|FOXP3|IL2RA|TGFB", data$interacting_pair, value = TRUE)
costimulatory <- grep("CD86|CD80|CD48|LILRB2|LILRB4|TNF|CD2|ICAM|SLAM|LT[AB]|NECTIN2|CD40|CD70|CD27|CD28|CD58|TSLP|PVR|CD44|CD55|CD[1-9]", data$interacting_pair, value = TRUE)
coinhibitory <- grep("SIRP|CD47|ICOS|TIGIT|CTLA4|PDCD1|CD274|LAG3|HAVCR|VSIR", data$interacting_pair, value = TRUE)
query_group <- list(
chemokines = chemokines,
chemokine = chemokines,
Expand All @@ -60,20 +76,21 @@ DEFAULT_COL_START <- 12
costimulation = costimulatory,
coinhibition = coinhibitory
)
query_group <- lapply(query_group, function(x) row.names(data[data$interacting_pair %in% x, ]))
if (!is.null(custom_gene_family)) {
cgf <- as.list(custom_gene_family)
cgf <- lapply(cgf, function(x) {
q_id <- grep(paste(x, collapse = "|"), data$interacting_pair)
q <- row.names(data)[q_id]
q_id <- grep(paste(x, collapse = "|"), data$interacting_pair, value = TRUE)
q <- row.names(data[data$interacting_pair %in% q_id, ])
return(q)
})
query_group <- c(query_group, cgf)
}
query <- NULL
} else if (is.null(gene_family) & !is.null(genes)) {
query_group <- NULL
query_id <- grep(paste(genes, collapse = "|"), data$interacting_pair)
query <- row.names(data)[query_id]
query_id <- grep(paste(genes, collapse = "|"), data$interacting_pair, value = TRUE)
query <- row.names(data[data$interacting_pair %in% query_id, ])
}
out <- list("query_group" = query_group, "query" = query)
return(out)
Expand All @@ -99,7 +116,7 @@ DEFAULT_COL_START <- 12

.prep_data_querygroup_celltype1 <- function(.data, .query_group, .gene_family, .cell_type, .celltype, ...) {
dat <- suppressWarnings(tryCatch(
.data[.query_group[[tolower(.gene_family)]],
.data[rownames(.data) %in% .query_group[[tolower(.gene_family)]],
grep(.cell_type, colnames(.data), useBytes = TRUE, ...),
drop = FALSE,
],
Expand All @@ -110,7 +127,7 @@ DEFAULT_COL_START <- 12
)
})
colidx <- unique(do.call(c, colidx))
tmpm <- .data[.query_group[[tolower(.gene_family)]], colidx, drop = FALSE]
tmpm <- .data[rownames(.data) %in% .query_group[[tolower(.gene_family)]], colidx, drop = FALSE]
return(tmpm)
}
))
Expand All @@ -120,7 +137,7 @@ DEFAULT_COL_START <- 12

.prep_data_querygroup_celltype2 <- function(.data, .query_group, .gene_family, .cell_type, .celltype, ...) {
dat <- suppressWarnings(tryCatch(
.data[unlist(.query_group[c(tolower(.gene_family))], use.names = FALSE),
.data[rownames(.data) %in% unlist(.query_group[c(tolower(.gene_family))], use.names = FALSE),
grep(.cell_type, colnames(.data), useBytes = TRUE, ...),
drop = FALSE
],
Expand All @@ -131,7 +148,7 @@ DEFAULT_COL_START <- 12
)
})
colidx <- unique(do.call(c, colidx))
tmpm <- .data[unlist(.query_group[c(tolower(.gene_family))], use.names = FALSE), colidx, drop = FALSE]
tmpm <- .data[rownames(.data) %in% unlist(.query_group[c(tolower(.gene_family))], use.names = FALSE), colidx, drop = FALSE]
return(tmpm)
}
))
Expand All @@ -140,7 +157,7 @@ DEFAULT_COL_START <- 12
}

.prep_data_query_celltype <- function(.data, .query, .cell_type, .celltype, ...) {
dat <- suppressWarnings(tryCatch(.data[.query, grep(.cell_type, colnames(.data),
dat <- suppressWarnings(tryCatch(.data[rownames(.data) %in% .query, grep(.cell_type, colnames(.data),
useBytes = TRUE, ...
), drop = FALSE], error = function(e) {
colidx <- lapply(.celltype, function(z) {
Expand All @@ -150,7 +167,7 @@ DEFAULT_COL_START <- 12
)
})
colidx <- unique(do.call(c, colidx))
tmpm <- .data[.query, colidx, drop = FALSE]
tmpm <- .data[rownames(.data) %in% .query, colidx, drop = FALSE]
return(tmpm)
}))
dat <- dat[rowSums(is.na(dat)) == 0, ]
Expand Down
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6 changes: 3 additions & 3 deletions man/plot_cpdb.Rd
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