Skip to content

Commit

Permalink
add function of plotting volcano plot for peptide level result
Browse files Browse the repository at this point in the history
  • Loading branch information
@hsiaoyi0504
hsiaoyi0504 committed Jul 2, 2024
1 parent 159e93c commit 44567d1
Show file tree
Hide file tree
Showing 2 changed files with 275 additions and 0 deletions.
1 change: 1 addition & 0 deletions NAMESPACE
View file
Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ export(plot_glycan_distribution)
export(plot_missval_heatmap)
export(plot_or)
export(plot_pca)
export(plot_peptide_volcano)
export(plot_volcano)
export(prepare_PTMSEA)
export(prepare_kinome)
Expand Down
274 changes: 274 additions & 0 deletions R/DE.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -616,6 +616,280 @@ plot_volcano <- function(dep, contrast, label_size = 3, name_col = NULL,
}
}

#' @export
plot_peptide_volcano <- function(dep, contrast, peptides=NA, show_other_peptides=T, show_gene=F,
label_size = 3, name_col = NULL,
add_names = TRUE, adjusted = T, alpha = 0.05, lfc = 1) {
# Show error if inputs are not the required classes
if (is.integer(label_size)) label_size <- as.numeric(label_size)
assertthat::assert_that(
inherits(dep, "SummarizedExperiment"),
is.character(contrast),
length(contrast) == 1,
is.numeric(label_size),
length(label_size) == 1,
is.logical(add_names),
length(add_names) == 1,
is.logical(adjusted),
length(adjusted) == 1,
metadata(se)$level == "peptide"
)

row_data <- rowData(dep, use.names = FALSE)

# Show error if inputs do not contain required columns
if (is.null(name_col)) {
name_col <- "ID"
}
if (any(!c("name", "ID", name_col) %in% colnames(row_data))) {
stop(
paste0(
"'name' and/or 'ID' columns are not present in '",
deparse(substitute(dep)),
"'.\nRun make_unique() to obtain required columns."
),
call. = FALSE
)
}

if (length(grep("_p.adj|_diff", colnames(row_data))) < 1) {
stop(
paste0(
"'[contrast]_diff' and '[contrast]_p.adj' columns are not present in '",
deparse(substitute(dep)),
"'.\nRun test_diff() to obtain the required columns."
),
call. = FALSE
)
}

if (length(grep("_significant", colnames(row_data))) < 1) {
stop(
paste0(
"'[contrast]_significant' columns are not present in '",
deparse(substitute(dep)),
"'.\nRun add_rejections() to obtain the required columns."
),
call. = FALSE
)
}

# Show error if an unvalid contrast is given
if (length(grep(
paste("^", contrast, "_diff", sep = ""),
colnames(row_data)
)) == 0) {
valid_cntrsts <- row_data %>%
data.frame() %>%
select(ends_with("_diff")) %>%
colnames(.) %>%
gsub("_diff", "", .)
valid_cntrsts_msg <- paste0(
"Valid contrasts are: '",
paste0(valid_cntrsts, collapse = "', '"),
"'"
)
stop("Not a valid contrast, please run `plot_volcano()` with a valid contrast as argument\n",
valid_cntrsts_msg,
call. = FALSE
)
}

# Generate a data.frame containing all info for the volcano plot
diff <- grep(
paste("^", contrast, "_diff", sep = ""),
colnames(row_data)
)
if (adjusted) {
p_values <- grep(
paste("^", contrast, "_p.adj", sep = ""),
colnames(row_data)
)
} else {
p_values <- grep(
paste("^", contrast, "_p.val", sep = ""),
colnames(row_data)
)
}
signif <- abs(row_data[, diff]) >= lfc & row_data[, p_values] <= alpha

df_tmp <- data.frame(
diff = row_data[, diff],
p_values = -log10(row_data[, p_values]),
signif = signif,
name = row_data$name,
ID = row_data$ID,
label = row_data[,name_col],
Gene = row_data$Gene
)

df <- df_tmp %>%
data.frame() %>%
filter(!is.na(signif)) %>%
arrange(signif)
name1 <- gsub("_vs_.*", "", contrast)
name2 <- gsub(".*_vs_", "", contrast)
# return(df)
# Plot volcano with or without labels
if (show_gene) {
df$ID_new <- paste0(df$Gene, gsub(".*_", "_", df$ID))
if (!show_other_peptides) {
p <- ggplot(df, aes(diff, p_values)) +
geom_vline(xintercept = 0) +
geom_point(aes(col = signif)) +
geom_point(data = subset(df, ID %in% c(peptides)), color = "maroon", size= 3) +
geom_text(data = data.frame(), aes(
x = c(Inf, -Inf),
y = c(-Inf, -Inf),
hjust = c(1, 0),
vjust = c(-1, -1),
label = c(name1, name2),
size = 5,
fontface = "bold"
)) +
geom_text_repel(data = subset(df, ID %in% peptides),
color = "maroon",
aes(label = ID_new)) +
labs(
title = contrast,
x = expression(log[2] ~ "Fold change")
) +
theme_bw() +
theme(panel.border = element_blank(), panel.grid.major = element_blank(),
panel.grid.minor = element_blank(), axis.line = element_line(colour = "black"), legend.position = "none") +
scale_color_manual(values = c("TRUE" = "black", "FALSE" = "grey"))
if (add_names) {
p <- p + ggrepel::geom_text_repel(
data = filter(df, signif),
aes(label = label),
size = label_size,
box.padding = unit(0.1, "lines"),
point.padding = unit(0.1, "lines"),
segment.size = 0.5
)
}
} else {
p <- ggplot(df, aes(diff, p_values)) +
geom_vline(xintercept = 0) +
geom_point(aes(col = signif)) +
geom_point(data = subset(df, gsub("_.*", "", ID) %in% c(gsub("_.*", "", peptides))),
color = "blue", size= 3) +
geom_point(data = subset(df, ID %in% peptides),
color = "maroon", size= 3) +
geom_text_repel(data = subset(df, ID %in% peptides),
color = "maroon",
aes(label = ID_new)) +
geom_text(data = data.frame(), aes(
x = c(Inf, -Inf),
y = c(-Inf, -Inf),
hjust = c(1, 0),
vjust = c(-1, -1),
label = c(name1, name2),
size = 5,
fontface = "bold"
)) +
labs(
title = contrast,
x = expression(log[2] ~ "Fold change")
) +
theme_bw() +
theme(panel.border = element_blank(), panel.grid.major = element_blank(),
panel.grid.minor = element_blank(), axis.line = element_line(colour = "black"), legend.position = "none") +
scale_color_manual(values = c("TRUE" = "black", "FALSE" = "grey"))
if (add_names) {
p <- p + ggrepel::geom_text_repel(
data = filter(df, signif),
aes(label = ID_new),
size = label_size,
box.padding = unit(0.1, "lines"),
point.padding = unit(0.1, "lines"),
segment.size = 0.5
)
}
}
} else {
if (!show_other_peptides) {
p <- ggplot(df, aes(diff, p_values)) +
geom_vline(xintercept = 0) +
geom_point(aes(col = signif)) +
geom_point(data = subset(df, ID %in% c(peptides)), color = "maroon", size= 3) +
geom_text(data = data.frame(), aes(
x = c(Inf, -Inf),
y = c(-Inf, -Inf),
hjust = c(1, 0),
vjust = c(-1, -1),
label = c(name1, name2),
size = 5,
fontface = "bold"
)) +
labs(
title = contrast,
x = expression(log[2] ~ "Fold change")
) +
theme_bw() +
theme(panel.border = element_blank(), panel.grid.major = element_blank(),
panel.grid.minor = element_blank(), axis.line = element_line(colour = "black"), legend.position = "none") +
scale_color_manual(values = c("TRUE" = "black", "FALSE" = "grey"))
if (add_names) {
p <- p + ggrepel::geom_text_repel(
data = filter(df, signif),
aes(label = label),
size = label_size,
box.padding = unit(0.1, "lines"),
point.padding = unit(0.1, "lines"),
segment.size = 0.5
)
}
} else {
p <- ggplot(df, aes(diff, p_values)) +
geom_vline(xintercept = 0) +
geom_point(aes(col = signif)) +
geom_point(data = subset(df, gsub("_.*", "", ID) %in% c(gsub("_.*", "", peptides))),
color = "blue", size= 3) +
geom_point(data = subset(df, ID %in% peptides),
color = "maroon", size= 3) +
geom_text_repel(data = subset(df, ID %in% peptides),
color = "maroon",
aes(label = ID)) +
geom_text(data = data.frame(), aes(
x = c(Inf, -Inf),
y = c(-Inf, -Inf),
hjust = c(1, 0),
vjust = c(-1, -1),
label = c(name1, name2),
size = 5,
fontface = "bold"
)) +
labs(
title = contrast,
x = expression(log[2] ~ "Fold change")
) +
theme_bw() +
theme(panel.border = element_blank(), panel.grid.major = element_blank(),
panel.grid.minor = element_blank(), axis.line = element_line(colour = "black"), legend.position = "none") +
scale_color_manual(values = c("TRUE" = "black", "FALSE" = "grey"))
if (add_names) {
p <- p + ggrepel::geom_text_repel(
data = filter(df, signif),
aes(label = label),
size = label_size,
box.padding = unit(0.1, "lines"),
point.padding = unit(0.1, "lines"),
segment.size = 0.5
)
}
}
}

if (adjusted) {
p <- p + labs(y = expression(-log[10] ~ "Adjusted p-value"))
} else {
p <- p + labs(y = expression(-log[10] ~ "P-value"))
}

return(p)
}

# From DEP
theme_DEP1 <- function() {
# Use theme_bw() as default
Expand Down

0 comments on commit 44567d1

Please sign in to comment.