R/treeplot.R
In YuLab-SMU/enrichplot: Visualization of Functional Enrichment Result
Defines functions
treeplot.compareClusterResult
treeplot.enrichResult
Documented in
treeplot.compareClusterResult
treeplot.enrichResult
##' @rdname treeplot
##' @exportMethod treeplot
setMethod("treeplot", signature(x = "enrichResult"),
function(x, ...) {
treeplot.enrichResult(x, ...)
})
##' @rdname treeplot
##' @exportMethod treeplot
setMethod("treeplot", signature(x = "gseaResult"),
function(x, ...) {
treeplot.enrichResult(x, ...)
})
##' @rdname treeplot
##' @exportMethod treeplot
setMethod("treeplot", signature(x = "compareClusterResult"),
function(x, ...) {
treeplot.compareClusterResult(x, ...)
})
##' @rdname treeplot
##' @param nWords The number of words in the cluster tags.
##' Will be removed in the next version.
##' @param nCluster The number of clusters, the default value is 5.
##' Will be removed in the next version.
##' @param cex_category Number indicating the amount by which plotting category.
##' nodes should be scaled relative to the default.
##' Will be removed in the next version.
##' @param label_format_cladelab label_format for group labels, a numeric value sets wrap length,
##' alternatively a custom function to format axis labels.
##' Will be removed in the next version.
##' @param label_format_tiplab label_format for tiplabs, a numeric value sets wrap length,
##' alternatively a custom function to format axis labels.
##' Will be removed in the next version.
##' @param offset_tiplab tiplab offset, rel object or numeric value, the bigger the number,
##' the farther the distance between the node and the branch.
##' The default is rel(1), when geneClusterPanel = "pie", meaning 1 * max_radius_of_the_pies;
##' when geneClusterPanel = "heatMap", meaning 1 * 0.16 * column_number_of_heatMap * x_range_of_tree;
##' when geneClusterPanel = "dotplot", meaning 1 * 0.09 * column_number_of_dotplot * x_range_of_tree.
##' Will be removed in the next version.
##' @param offset rel object or numeric value, distance bar and tree,
##' offset of bar and text from the clade, default is rel(1),
##' meaning 1 * 1.2 * x_range_of_tree plus distance_between_tree_and_tiplab
##' (1 * (1.2 * x_range_of_tree + distance_between_tree_and_tiplab)).
##' Will be removed in the next version.
##' @param fontsize The size of text, default is 4.
##' @param hclust_method Method of hclust. This should be (an unambiguous abbreviation of) one of "ward.D",
##' "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).
##' Will be removed in the next version.
##' @param group_color A vector of group colors, the length of the vector should be the same as nCluster.
##' Will be removed in the next version.
##' @param extend Numeric, extend the length of bar, default is 0.3.
##' Will be removed in the next version.
##' @param hilight Logical value, if TRUE(default), add ggtree::geom_hilight() layer.
##' Will be removed in the next version.
##' @param hexpand expand x limits by amount of xrange * hexpand.
##' Will be removed in the next version.
##' @param align control the align direction of the edge of high light rectangular.
##' Options is 'none', 'left', 'right', 'both (default)'.
##' Will be removed in the next version.
##' @param hilight.params list, the parameters to control the attributes of highlight layer.
##' see the hilight.params in the following.
##' hilight.params control the attributes of highlight layer, it can be referred to the following parameters:
##' \itemize{
##' \item \code{hilight} Logical value, if TRUE(default), add ggtree::geom_hilight() layer.
##' \item \code{align} control the align direction of the edge of high light rectangular.
##' Options is 'none', 'left', 'right', 'both (default)'.
##' }
##' @param offset.params list, the parameters to control the offset.
##' see the offset.params in the following.
##' offset.params control the attributes of offset, it can be referred to the following parameters:
##' \itemize{
##' \item \code{bar_tree} rel object or numeric value, distance bar and tree,
##' offset of bar and text from the clade, default is rel(1),
##' meaning 1 * 1.2 * x_range_of_tree plus distance_between_tree_and_tiplab
##' (1 * (1.2 * x_range_of_tree + distance_between_tree_and_tiplab)).
##' \item \code{tiplab} tiplab offset, rel object or numeric value, the bigger the number,
##' the farther the distance between the node and the branch.
##' The default is rel(1), when clusterPanel = "pie", meaning 1 * max_radius_of_the_pies;
##' when clusterPanel = "heatMap", meaning 1 * 0.16 * column_number_of_heatMap * x_range_of_tree;
##' when clusterPanel = "dotplot", meaning 1 * 0.09 * column_number_of_dotplot * x_range_of_tree.
##' \item \code{extend} Numeric, extend the length of bar, default is 0.3.
##' \item \code{hexpand} expand x limits by amount of xrange * hexpand.
##' }
##' @param cluster.params list, the parameters to control the attributes of highlighted nodes and edges.
##' see the cluster.params in the following.
##' cluster.params control the attributes of highlight, it can be referred to the following parameters:
##' \itemize{
##' \item \code{method} function of Clustering method, such as stats::kmeans(the default),
##' cluster::clara, cluster::fanny or cluster::pam.
##' \item \code{n} Numeric, the number of clusters,
##' the default value is square root of the number of nodes.
##' \item \code{color} A vector of group colors, the length of the vector should be the same as nCluster.
##' \item \code{label_words_n} Numeric, the number of words in the cluster tags, the default value is 4.
##' \item \code{label_format} A numeric value sets wrap length, alternatively a
##' custom function to format axis labels.
##' }
##' @importFrom ggtree %<+%
##' @importFrom ggtree ggtree
##' @importFrom ggtree geom_tiplab
##' @importFrom ggtree geom_tippoint
##' @importFrom ggtree groupClade
##' @importFrom ggtree geom_cladelab
##' @importFrom ggplot2 coord_cartesian
##' @importFrom ggplot2 scale_colour_continuous
##'
treeplot.enrichResult <- function(x,
showCategory = 30,
color = "p.adjust",
nWords = 4, # removed
nCluster = 5, # removed
cex_category = 1,
label_format = NULL,
label_format_cladelab = 30, # removed
label_format_tiplab = NULL,
fontsize = 4,
offset = rel(1), # removed
offset_tiplab = rel(1), # removed
hclust_method = "ward.D", # removed
group_color = NULL, # removed
extend = 0.3, # removed
hilight = TRUE, # removed
hexpand = .1, # removed
align = "both", # removed
hilight.params = list(
hilight = TRUE,
align = "both"
),
offset.params = list(
bar_tree = rel(1),
tiplab = rel(1),
extend = 0.3,
hexpand = .1
),
cluster.params = list(
method = "ward.D",
n = 5,
color = NULL,
label_words_n = 4,
label_format = 30
),
...) {
# change parameter name
##############################################################
params_df <- as.data.frame(rbind(
c("hilight", "hilight.params", "hilight"),
c("align", "hilight.params", "align"),
c("offset", "offset.params", "bar_tree"),
c("offset_tiplab", "offset.params", "tiplab"),
c("extend", "offset.params", "extend"),
c("hexpand", "offset.params", "hexpand"),
c("hclust_method", "cluster.params", "method"),
c("nCluster", "cluster.params", "n"),
c("group_color", "cluster.params", "color"),
c("nWords", "cluster.params", "label_words_n"),
c("label_format_cladelab", "cluster.params", "label_format"))
)
colnames(params_df) <- c("original", "listname", "present")
rownames(params_df) <- params_df$original
default.hilight.params <- list(
hilight = TRUE,
align = "both"
)
default.offset.params <- list(
bar_tree = rel(1),
tiplab = rel(1),
extend = 0.3,
hexpand = .1
)
default.cluster.params <- list(
method = "ward.D",
n = 5,
color = NULL,
label_words_n = 4,
label_format = 30
)
# use modifyList to change the values of parameter
hilight.params <- modifyList(default.hilight.params, hilight.params)
offset.params <- modifyList(default.offset.params, offset.params)
cluster.params <- modifyList(default.cluster.params, cluster.params)
params_list <- list(x = x,
showCategory = showCategory,
color = color,
nWords = nWords,
nCluster = nCluster,
cex_category = cex_category,
label_format = label_format,
label_format_cladelab = label_format_cladelab,
label_format_tiplab = label_format_tiplab,
fontsize = fontsize,
offset = offset,
offset_tiplab = offset_tiplab,
hclust_method = hclust_method,
group_color = group_color,
extend = extend,
hilight = hilight,
hexpand = hexpand,
align = align,
hilight.params = hilight.params,
offset.params = offset.params,
cluster.params = cluster.params
)
# get all parameters value
args <- as.list(match.call())
removed_params <- intersect(params_df$original, names(args))
if (length(removed_params) > 0) {
for (i in removed_params) {
params_list[[params_df[i, 2]]][[params_df[i, 3]]] <- get(i)
warn <- get_param_change_message(i, params_df)
warning(warn)
}
}
hilight.params <- params_list[["hilight.params"]]
offset.params <- params_list[["offset.params"]]
cluster.params <- params_list[["cluster.params"]]
hilight <- hilight.params[["hilight"]]
align <- hilight.params[["align"]]
offset <- offset.params[["bar_tree"]]
offset_tiplab <- offset.params[["tiplab"]]
extend <- offset.params[["extend"]]
hexpand <- offset.params[["hexpand"]]
hclust_method <- cluster.params[["method"]]
nCluster <- cluster.params[["n"]]
group_color <- cluster.params[["color"]]
nWords <- cluster.params[["label_words_n"]]
label_format_cladelab <- cluster.params[["label_format"]]
group <- p.adjust <- count<- NULL
# to compatible with older versions
if (!is.null(label_format)) {
label_format_cladelab <- label_format
}
# if (class(x) == "gseaResult")
if (inherits(x, "gseaResult")) {
x@result$Count <- x$core_enrichment %>%
strsplit(split = "/") %>%
vapply(length, FUN.VALUE = 1)
}
n <- update_n(x, showCategory)
if (is.numeric(n)) {
keep <- seq_len(n)
} else {
keep <- match(n, rownames(x@termsim))
}
if (length(keep) == 0) {
stop("no enriched term found...")
}
## Fill the upper triangular matrix completely
termsim2 <- fill_termsim(x, keep)
## Use the ward.D method to avoid overlapping ancestor nodes of each group
hc <- stats::hclust(stats::as.dist(1- termsim2),
method = hclust_method)
clus <- stats::cutree(hc, nCluster)
d <- data.frame(label = names(clus),
#node = seq_len(length(clus)),
color = x[keep, as.character(color)],
count = x$Count[keep])
## Group the nodes.
p <- group_tree(hc = hc, clus = clus, d = d, offset_tiplab = offset_tiplab,
nWords = nWords, label_format_cladelab = label_format_cladelab,
label_format_tiplab = label_format_tiplab, offset = offset,
fontsize = fontsize, group_color = group_color, extend = extend,
hilight = hilight, cex_category = cex_category, align = align, align_tiplab = FALSE,
color = color)
# xlim <- c(0, xlim * 3 * max(p$data$x))
# p + coord_cartesian(xlim = xlim) +
# p + ggnewscale::new_scale_colour() +
# geom_tippoint(aes(color = color, size = count)) +
p + scale_size_continuous(name = "number of genes",
range = c(3, 8) * cex_category) +
ggtree::hexpand(ratio = hexpand) +
guides(size = guide_legend(order = 1),
color = guide_colorbar(order = 2))
}
##' @rdname treeplot
##' @param split Separate result by 'category' variable.
##' @param legend_n Number of circle in legend, the default value is 3.
##' Will be removed in the next version.
##' @param geneClusterPanel one of "heatMap"(default), "dotplot", "pie".
##' Will be removed in the next version.
##' @param pie Used only when geneClusterPanel = "pie",
##' proportion of clusters in the pie chart, one of 'equal' (default) and 'Count'.
##' Will be removed in the next version.
##' @param clusterPanel.params list, the parameters to control the attributes of cluster panel.
##' see the clusterPanel.params in the following.
##' clusterPanel.params control the attributes of cluster panel, it can be referred to the following parameters:
##' \itemize{
##' \item \code{clusterPanel} one of "heatMap"(default), "dotplot", "pie".
##' \item \code{pie} pUsed only when ClusterPanel = "pie",
##' proportion of clusters in the pie chart, one of 'equal' (default) and 'Count'.
##' \item \code{legend_n} number of circle in legend.
##' \item \code{colnames_angle} set the angle of colnames.
##' }
##' @importFrom ggtree nodepie
##' @importFrom ggtree geom_inset
##' @importFrom ggplot2 scale_fill_manual
##' @importFrom rlang check_installed
treeplot.compareClusterResult <- function(x,
showCategory = 5,
color = "p.adjust",
nWords = 4, # removed
nCluster = 5, # removed
cex_category = 1,
split = NULL,
label_format = NULL,
label_format_cladelab = 30, # removed
label_format_tiplab = NULL,
fontsize = 4,
offset = rel(1), # removed
pie = "equal", # removed
legend_n = 3, # removed
offset_tiplab = rel(1), # removed
hclust_method = "ward.D", # removed
group_color = NULL, # removed
extend = 0.3, # removed
hilight = TRUE, # removed
geneClusterPanel = "heatMap", # removed
hexpand = .1, # removed
align = "both", # removed
cluster.params = list(
method = "ward.D",
n = 5,
color = NULL,
label_words_n = 4,
label_format = 30
),
hilight.params = list(
hilight = TRUE,
align = "both"
),
clusterPanel.params = list(
clusterPanel = "heatMap",
pie = "equal",
legend_n = 3,
colnames_angle = 0
),
offset.params = list(
bar_tree = rel(1),
tiplab = rel(1),
extend = 0.3,
hexpand = .1
),...) {
# change parameter name
##############################################################
params_df <- as.data.frame(rbind(
c("hclust_method", "cluster.params", "method"),
c("nCluster", "cluster.params", "n"),
c("group_color", "cluster.params", "color"),
c("nWords", "cluster.params", "label_words_n"),
c("label_format_cladelab", "cluster.params", "label_format"),
c("hilight", "hilight.params", "hilight"),
c("align", "hilight.params", "align"),
c("geneClusterPanel", "clusterPanel.params", "clusterPanel"),
c("pie", "clusterPanel.params", "pie"),
c("legend_n", "clusterPanel.params", "legend_n"),
c("offset", "offset.params", "bar_tree"),
c("offset_tiplab", "offset.params", "tiplab"),
c("extend", "offset.params", "extend"),
c("hexpand", "offset.params", "hexpand"))
)
colnames(params_df) <- c("original", "listname", "present")
rownames(params_df) <- params_df$original
default.cluster.params <- list(
method = "ward.D",
n = 5,
color = NULL,
label_words_n = 4,
label_format = 30
)
default.hilight.params <- list(
hilight = TRUE,
align = "both"
)
default.clusterPanel.params <- list(
clusterPanel = "heatMap",
pie = "equal",
legend_n = 3,
colnames_angle = 0
)
default.offset.params <- list(
bar_tree = rel(1),
tiplab = rel(1),
extend = 0.3,
hexpand = .1
)
# use modifyList to change the values of parameter
cluster.params <- modifyList(default.cluster.params, cluster.params)
hilight.params <- modifyList(default.hilight.params, hilight.params)
clusterPanel.params <- modifyList(default.clusterPanel.params, clusterPanel.params)
offset.params <- modifyList(default.offset.params, offset.params)
params_list <- list(x = x,
showCategory = showCategory,
color = color,
nWords = nWords,
nCluster = nCluster,
cex_category = cex_category,
split = split,
label_format = label_format,
label_format_cladelab = label_format_cladelab,
label_format_tiplab = label_format_tiplab,
fontsize = fontsize,
offset = offset,
pie = pie,
legend_n = legend_n,
offset_tiplab = offset_tiplab,
hclust_method = hclust_method,
group_color = group_color,
extend = extend,
hilight = hilight,
geneClusterPanel = geneClusterPanel,
hexpand = hexpand,
align = align,
cluster.params = cluster.params,
hilight.params = hilight.params,
clusterPanel.params = clusterPanel.params,
offset.params = offset.params
)
# get all parameters value
args <- as.list(match.call())
removed_params <- intersect(params_df$original, names(args))
if (length(removed_params) > 0) {
for (i in removed_params) {
params_list[[params_df[i, 2]]][[params_df[i, 3]]] <- get(i)
warn <- get_param_change_message(i, params_df)
warning(warn)
}
}
cluster.params <- params_list[["cluster.params"]]
hilight.params <- params_list[["hilight.params"]]
clusterPanel.params <- params_list[["clusterPanel.params"]]
offset.params <- params_list[["offset.params"]]
hclust_method <- cluster.params[["method"]]
nCluster <- cluster.params[["n"]]
group_color <- cluster.params[["color"]]
nWords <- cluster.params[["label_words_n"]]
label_format_cladelab <- cluster.params[["label_format"]]
hilight <- hilight.params[["hilight"]]
align <- hilight.params[["align"]]
geneClusterPanel <- clusterPanel.params[["clusterPanel"]]
pie <- clusterPanel.params[["pie"]]
legend_n <- clusterPanel.params[["legend_n"]]
colnames_angle <- clusterPanel.params[["colnames_angle"]]
hilight <- hilight.params[["hilight"]]
align <- hilight.params[["align"]]
offset <- offset.params[["bar_tree"]]
offset_tiplab <- offset.params[["tiplab"]]
extend <- offset.params[["extend"]]
hexpand <- offset.params[["hexpand"]]
# geneClusterPanel <- match.arg(geneClusterPanel, c("heatMap", "dotplot", "pie"))
has_pairsim(x)
group <- Description <- Cluster <- Count <- NULL
# to compatible with older versions
if (!is.null(label_format)) {
label_format_cladelab <- label_format
}
# y <- get_selected_category(showCategory, x, split)
y <- fortify(x, showCategory = showCategory,
includeAll = TRUE, split = split)
y$Cluster <- sub("\n.*", "", y$Cluster)
if ("core_enrichment" %in% colnames(y)) { ## for GSEA result
y$geneID <- y$core_enrichment
}
## Data structure transformation, combining the same ID (Description) genes
merged_ggData <- merge_compareClusterResult(y)
ID_Cluster_mat <- prepare_pie_category(y, pie=pie)
## Fill the upper triangular matrix completely
termsim2 <- fill_termsim(x, rownames(ID_Cluster_mat))
hc <- stats::hclust(stats::as.dist(1- termsim2),
method = hclust_method)
clus <- stats::cutree(hc, nCluster)
rownames(merged_ggData) <- merged_ggData$Description
d <- data.frame(label = names(clus),
count = merged_ggData[names(clus), "Count"])
p <- group_tree(hc = hc, clus = clus, d = d, offset_tiplab = offset_tiplab,
nWords = nWords, label_format_cladelab = label_format_cladelab,
label_format_tiplab = label_format_tiplab, offset = offset,
fontsize = fontsize, group_color = group_color, extend = extend,
hilight = hilight, cex_category = cex_category, ID_Cluster_mat = ID_Cluster_mat,
geneClusterPanel = geneClusterPanel, align = align, add_tippoint = FALSE,
align_tiplab = TRUE, color = color)
p_data <- as.data.frame(p$data)
p_data <- p_data[which(!is.na(p_data$label)), ]
rownames(p_data) <- p_data$label
p_data <- p_data[rownames(ID_Cluster_mat), ]
# if (geneClusterPanel == "pie") {
# xlim <- c(0, xlim * 3 * p_data$x[1])
# } else {
# xlim <- c(0, xlim * 4.5 * p_data$x[1])
# }
if (geneClusterPanel == "pie") {
ID_Cluster_mat$radius <- sqrt(p_data$count / sum(p_data$count) * cex_category)
ID_Cluster_mat$x <- p_data$x
ID_Cluster_mat$y <- p_data$y
ID_Cluster_mat$node <- p_data$node
p <- p + ggnewscale::new_scale_fill() +
scatterpie::geom_scatterpie(aes_(x=~x,y=~y,r=~radius), data=ID_Cluster_mat,
cols=colnames(ID_Cluster_mat)[1:(ncol(ID_Cluster_mat)-4)],color=NA) +
scatterpie::geom_scatterpie_legend(ID_Cluster_mat$radius,
x = 0.8, y = 0.1, n = legend_n,
labeller = function(x) round(sum(p_data$count) * x^2 / cex_category)) +
# coord_equal(xlim = xlim) +
labs(fill = "Cluster") + coord_equal()
}
if (geneClusterPanel == "heatMap") {
heatMapData <- as.data.frame(x)
heatMapData$Cluster <- as.character(heatMapData$Cluster)
heatMapData <- heatMapData[heatMapData$Cluster %in% colnames(ID_Cluster_mat), ]
heatMapData <- heatMapData[heatMapData$Description %in% rownames(ID_Cluster_mat), ]
for (i in seq_len(nrow(heatMapData))) {
ID_Cluster_mat[heatMapData[i, "Description"], heatMapData[i, "Cluster"]] <- heatMapData[i, color]
}
p <- p + ggnewscale::new_scale_fill() # +
# coord_equal(xlim = xlim)
p <- ggtree::gheatmap(p, ID_Cluster_mat, colnames_angle = colnames_angle) +
# scale_fill_continuous(trans = "log10", name = color) +
set_enrichplot_color(type = "fill", trans = "log10", name = color)
}
if (geneClusterPanel == "dotplot") {
dotdata <- as.data.frame(x)
pData <- as.data.frame(p$data)
paths <- pData$label[order(pData$y, decreasing = TRUE)] %>% .[!is.na(.)]
dotdata <- dotdata[dotdata$Description %in% paths, ]
dotdata <- dplyr::select(dotdata, Description, dplyr::everything())
check_installed("ggtreeExtra", "for `treeplot()` with ` clusterPanel = 'dotplot'`.")
p <- p + ggnewscale::new_scale_colour() +
ggtreeExtra::geom_fruit(data = dotdata, geom = geom_point,
mapping = aes_string(x = "Cluster", y = "Description",
size = "Count", color = color),
# pwidth = 0.5, offset = -0.2,
pwidth = 0.06*ncol(ID_Cluster_mat),
axis.params = list(axis = "x", text.size = 3, line.alpha = 0, text.angle = colnames_angle)) +
# scale_colour_continuous(trans = "log10", name = color) +
set_enrichplot_color(trans = "log10", name = color)
}
p + ggtree::hexpand(ratio = hexpand)
}
##' Fill the upper triangular matrix completely
##'
##' @param x enrichment result
##' @param keep keep value
##'
##' @return a data.frame
##' @noRd
fill_termsim <- function(x, keep) {
termsim <- x@termsim[keep, keep]
termsim[which(is.na(termsim))] <- 0
termsim2 <- termsim + t(termsim)
for ( i in seq_len(nrow(termsim2)))
termsim2[i, i] <- 1
return(termsim2)
}
##' Add geom_cladelab() to a ggtree object.
##'
##' @param p a ggtree object
##' @param nWords the number of words in the cluster tags
##' @param label_format a numeric value sets wrap length, alternatively a
##' custom function to format axis labels.
##' @param offset offset of bar and text from the clade.
##' @importFrom rlang check_installed
##'
##' @return a ggtree object
##' @noRd
add_cladelab <- function(p, nWords, label_format_cladelab,
offset, roots,
fontsize, group_color, cluster_color,
pdata, extend, hilight, align) {
# align <- getOption("enriplot.treeplot.align", default = "both")
cluster_label <- sapply(cluster_color, get_wordcloud, ggData = pdata,
nWords = nWords)
label_func_cladelab <- default_labeller(label_format_cladelab)
if (is.function(label_format_cladelab)) {
label_func_cladelab <- label_format_cladelab
}
cluster_label <- label_func_cladelab(cluster_label)
n_color <- length(levels(cluster_color)) - length(cluster_color)
if (is.null(group_color)) {
check_installed('scales', 'for `add_cladelab()`.')
color2 <- scales::hue_pal()(length(roots) + n_color)
if (n_color > 0) color2 <- color2[-seq_len(n_color)]
} else {
color2 <- group_color
}
df <- data.frame(node = as.numeric(roots),
labels = cluster_label,
cluster=cluster_color,
# color = scales::hue_pal()(length(roots) + n_color)[-seq_len(n_color)]
color = color2
)
p <- p + ggnewscale::new_scale_colour() +
geom_cladelab(
data = df,
mapping = aes_(node =~ node, label =~ labels, color =~ cluster),
textcolor = "black",
extend = extend,
show.legend = FALSE,
fontsize = fontsize, offset = offset) +
scale_color_manual(values = df$color,
guide = 'none')
if (hilight) {
p <- p + ggtree::geom_hilight(
data = df,
mapping = aes_(node =~ node, fill =~ cluster),
show.legend = FALSE,
align = align) +
scale_fill_manual(values = df$color,
guide = 'none')
}
return(p)
}
##' Group the nodes.
##'
##' @return a ggtree object
##' @noRd
group_tree <- function(hc, clus, d, offset_tiplab, nWords,
label_format_cladelab, label_format_tiplab,
offset, fontsize, group_color,
extend, hilight, cex_category,
ID_Cluster_mat = NULL, geneClusterPanel = NULL,
align, add_tippoint = TRUE, align_tiplab = TRUE, color) {
group <- count <- NULL
# cluster data
dat <- data.frame(name = names(clus), cls=paste0("cluster_", as.numeric(clus)))
grp <- apply(table(dat), 2, function(x) names(x[x == 1]))
p <- ggtree(hc, hang=-1, branch.length = "none", show.legend=FALSE)
# extract the most recent common ancestor
noids <- lapply(grp, function(x) unlist(lapply(x, function(i) ggtree::nodeid(p, i))))
roots <- unlist(lapply(noids, function(x) ggtree::MRCA(p, x)))
# cluster data
p <- ggtree::groupOTU(p, grp, "group") + aes_(color =~ group)
rangeX <- max(p$data$x, na.rm=TRUE) - min(p$data$x, na.rm=TRUE)
if (inherits(offset_tiplab, "rel")) {
offset_tiplab <- unclass(offset_tiplab)
if (geneClusterPanel == "pie" || is.null(geneClusterPanel)) {
## 1.5 * max(radius_of_pie)
offset_tiplab <- offset_tiplab * .5 * max(sqrt(d$count / sum(d$count) * cex_category))
} else if (geneClusterPanel == "heatMap") {
## Close to the width of the tree
offset_tiplab <- offset_tiplab * 0.2 * ncol(ID_Cluster_mat) * rangeX
} else if (geneClusterPanel == "dotplot") {
## Close to the width of the tree
offset_tiplab <- offset_tiplab * 0.09 * ncol(ID_Cluster_mat) * rangeX
}
}
if (inherits(offset, "rel")) {
offset <- unclass(offset)
offset <- offset * rangeX * 1.2 + offset_tiplab
}
# max_nchar <- max(nchar(p$data$label), na.rm = TRUE)
pdata <- data.frame(name = p$data$label, color2 = p$data$group)
pdata <- pdata[!is.na(pdata$name), ]
cluster_color <- unique(pdata$color2)
n_color <- length(levels(cluster_color)) - length(cluster_color)
if (!is.null(group_color)) {
color2 <- c(rep("black", n_color), group_color)
p <- p + scale_color_manual(values = color2, guide = 'none')
}
p <- p %<+% d
if (!is.null(label_format_tiplab)) {
label_func_tiplab <- default_labeller(label_format_tiplab)
if (is.function(label_format_tiplab)) {
label_func_tiplab <- label_format_tiplab
}
isTip <- p$data$isTip
p$data$label[isTip] <- label_func_tiplab(p$data$label[isTip])
}
p <- add_cladelab(p = p, nWords = nWords,
label_format_cladelab = label_format_cladelab,
offset = offset, roots = roots, fontsize = fontsize,
group_color = group_color, cluster_color = cluster_color,
pdata = pdata, extend = extend, hilight = hilight, align = align)
if (add_tippoint) {
p <- p + ggnewscale::new_scale_colour() +
geom_tippoint(aes(color = color, size = count)) +
# scale_colour_continuous(name = color)+
set_enrichplot_color(name = color)
}
## add tiplab
p <- p + geom_tiplab(offset = offset_tiplab, hjust = 0,
show.legend = FALSE, align = align_tiplab, linesize = 0)
return(p)
}
YuLab-SMU/enrichplot documentation built on Jan. 10, 2025, 4:44 a.m.
R Package Documentation
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Defines functions treeplot.compareClusterResult treeplot.enrichResult
Documented in treeplot.compareClusterResult treeplot.enrichResult
##' @rdname treeplot
##' @exportMethod treeplot
setMethod("treeplot", signature(x = "enrichResult"),
function(x, ...) {
treeplot.enrichResult(x, ...)
})
##' @rdname treeplot
##' @exportMethod treeplot
setMethod("treeplot", signature(x = "gseaResult"),
function(x, ...) {
treeplot.enrichResult(x, ...)
})
##' @rdname treeplot
##' @exportMethod treeplot
setMethod("treeplot", signature(x = "compareClusterResult"),
function(x, ...) {
treeplot.compareClusterResult(x, ...)
})
##' @rdname treeplot
##' @param nWords The number of words in the cluster tags.
##' Will be removed in the next version.
##' @param nCluster The number of clusters, the default value is 5.
##' Will be removed in the next version.
##' @param cex_category Number indicating the amount by which plotting category.
##' nodes should be scaled relative to the default.
##' Will be removed in the next version.
##' @param label_format_cladelab label_format for group labels, a numeric value sets wrap length,
##' alternatively a custom function to format axis labels.
##' Will be removed in the next version.
##' @param label_format_tiplab label_format for tiplabs, a numeric value sets wrap length,
##' alternatively a custom function to format axis labels.
##' Will be removed in the next version.
##' @param offset_tiplab tiplab offset, rel object or numeric value, the bigger the number,
##' the farther the distance between the node and the branch.
##' The default is rel(1), when geneClusterPanel = "pie", meaning 1 * max_radius_of_the_pies;
##' when geneClusterPanel = "heatMap", meaning 1 * 0.16 * column_number_of_heatMap * x_range_of_tree;
##' when geneClusterPanel = "dotplot", meaning 1 * 0.09 * column_number_of_dotplot * x_range_of_tree.
##' Will be removed in the next version.
##' @param offset rel object or numeric value, distance bar and tree,
##' offset of bar and text from the clade, default is rel(1),
##' meaning 1 * 1.2 * x_range_of_tree plus distance_between_tree_and_tiplab
##' (1 * (1.2 * x_range_of_tree + distance_between_tree_and_tiplab)).
##' Will be removed in the next version.
##' @param fontsize The size of text, default is 4.
##' @param hclust_method Method of hclust. This should be (an unambiguous abbreviation of) one of "ward.D",
##' "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).
##' Will be removed in the next version.
##' @param group_color A vector of group colors, the length of the vector should be the same as nCluster.
##' Will be removed in the next version.
##' @param extend Numeric, extend the length of bar, default is 0.3.
##' Will be removed in the next version.
##' @param hilight Logical value, if TRUE(default), add ggtree::geom_hilight() layer.
##' Will be removed in the next version.
##' @param hexpand expand x limits by amount of xrange * hexpand.
##' Will be removed in the next version.
##' @param align control the align direction of the edge of high light rectangular.
##' Options is 'none', 'left', 'right', 'both (default)'.
##' Will be removed in the next version.
##' @param hilight.params list, the parameters to control the attributes of highlight layer.
##' see the hilight.params in the following.
##' hilight.params control the attributes of highlight layer, it can be referred to the following parameters:
##' \itemize{
##' \item \code{hilight} Logical value, if TRUE(default), add ggtree::geom_hilight() layer.
##' \item \code{align} control the align direction of the edge of high light rectangular.
##' Options is 'none', 'left', 'right', 'both (default)'.
##' }
##' @param offset.params list, the parameters to control the offset.
##' see the offset.params in the following.
##' offset.params control the attributes of offset, it can be referred to the following parameters:
##' \itemize{
##' \item \code{bar_tree} rel object or numeric value, distance bar and tree,
##' offset of bar and text from the clade, default is rel(1),
##' meaning 1 * 1.2 * x_range_of_tree plus distance_between_tree_and_tiplab
##' (1 * (1.2 * x_range_of_tree + distance_between_tree_and_tiplab)).
##' \item \code{tiplab} tiplab offset, rel object or numeric value, the bigger the number,
##' the farther the distance between the node and the branch.
##' The default is rel(1), when clusterPanel = "pie", meaning 1 * max_radius_of_the_pies;
##' when clusterPanel = "heatMap", meaning 1 * 0.16 * column_number_of_heatMap * x_range_of_tree;
##' when clusterPanel = "dotplot", meaning 1 * 0.09 * column_number_of_dotplot * x_range_of_tree.
##' \item \code{extend} Numeric, extend the length of bar, default is 0.3.
##' \item \code{hexpand} expand x limits by amount of xrange * hexpand.
##' }
##' @param cluster.params list, the parameters to control the attributes of highlighted nodes and edges.
##' see the cluster.params in the following.
##' cluster.params control the attributes of highlight, it can be referred to the following parameters:
##' \itemize{
##' \item \code{method} function of Clustering method, such as stats::kmeans(the default),
##' cluster::clara, cluster::fanny or cluster::pam.
##' \item \code{n} Numeric, the number of clusters,
##' the default value is square root of the number of nodes.
##' \item \code{color} A vector of group colors, the length of the vector should be the same as nCluster.
##' \item \code{label_words_n} Numeric, the number of words in the cluster tags, the default value is 4.
##' \item \code{label_format} A numeric value sets wrap length, alternatively a
##' custom function to format axis labels.
##' }
##' @importFrom ggtree %<+%
##' @importFrom ggtree ggtree
##' @importFrom ggtree geom_tiplab
##' @importFrom ggtree geom_tippoint
##' @importFrom ggtree groupClade
##' @importFrom ggtree geom_cladelab
##' @importFrom ggplot2 coord_cartesian
##' @importFrom ggplot2 scale_colour_continuous
##'
treeplot.enrichResult <- function(x,
showCategory = 30,
color = "p.adjust",
nWords = 4, # removed
nCluster = 5, # removed
cex_category = 1,
label_format = NULL,
label_format_cladelab = 30, # removed
label_format_tiplab = NULL,
fontsize = 4,
offset = rel(1), # removed
offset_tiplab = rel(1), # removed
hclust_method = "ward.D", # removed
group_color = NULL, # removed
extend = 0.3, # removed
hilight = TRUE, # removed
hexpand = .1, # removed
align = "both", # removed
hilight.params = list(
hilight = TRUE,
align = "both"
),
offset.params = list(
bar_tree = rel(1),
tiplab = rel(1),
extend = 0.3,
hexpand = .1
),
cluster.params = list(
method = "ward.D",
n = 5,
color = NULL,
label_words_n = 4,
label_format = 30
),
...) {
# change parameter name
##############################################################
params_df <- as.data.frame(rbind(
c("hilight", "hilight.params", "hilight"),
c("align", "hilight.params", "align"),
c("offset", "offset.params", "bar_tree"),
c("offset_tiplab", "offset.params", "tiplab"),
c("extend", "offset.params", "extend"),
c("hexpand", "offset.params", "hexpand"),
c("hclust_method", "cluster.params", "method"),
c("nCluster", "cluster.params", "n"),
c("group_color", "cluster.params", "color"),
c("nWords", "cluster.params", "label_words_n"),
c("label_format_cladelab", "cluster.params", "label_format"))
)
colnames(params_df) <- c("original", "listname", "present")
rownames(params_df) <- params_df$original
default.hilight.params <- list(
hilight = TRUE,
align = "both"
)
default.offset.params <- list(
bar_tree = rel(1),
tiplab = rel(1),
extend = 0.3,
hexpand = .1
)
default.cluster.params <- list(
method = "ward.D",
n = 5,
color = NULL,
label_words_n = 4,
label_format = 30
)
# use modifyList to change the values of parameter
hilight.params <- modifyList(default.hilight.params, hilight.params)
offset.params <- modifyList(default.offset.params, offset.params)
cluster.params <- modifyList(default.cluster.params, cluster.params)
params_list <- list(x = x,
showCategory = showCategory,
color = color,
nWords = nWords,
nCluster = nCluster,
cex_category = cex_category,
label_format = label_format,
label_format_cladelab = label_format_cladelab,
label_format_tiplab = label_format_tiplab,
fontsize = fontsize,
offset = offset,
offset_tiplab = offset_tiplab,
hclust_method = hclust_method,
group_color = group_color,
extend = extend,
hilight = hilight,
hexpand = hexpand,
align = align,
hilight.params = hilight.params,
offset.params = offset.params,
cluster.params = cluster.params
)
# get all parameters value
args <- as.list(match.call())
removed_params <- intersect(params_df$original, names(args))
if (length(removed_params) > 0) {
for (i in removed_params) {
params_list[[params_df[i, 2]]][[params_df[i, 3]]] <- get(i)
warn <- get_param_change_message(i, params_df)
warning(warn)
}
}
hilight.params <- params_list[["hilight.params"]]
offset.params <- params_list[["offset.params"]]
cluster.params <- params_list[["cluster.params"]]
hilight <- hilight.params[["hilight"]]
align <- hilight.params[["align"]]
offset <- offset.params[["bar_tree"]]
offset_tiplab <- offset.params[["tiplab"]]
extend <- offset.params[["extend"]]
hexpand <- offset.params[["hexpand"]]
hclust_method <- cluster.params[["method"]]
nCluster <- cluster.params[["n"]]
group_color <- cluster.params[["color"]]
nWords <- cluster.params[["label_words_n"]]
label_format_cladelab <- cluster.params[["label_format"]]
group <- p.adjust <- count<- NULL
# to compatible with older versions
if (!is.null(label_format)) {
label_format_cladelab <- label_format
}
# if (class(x) == "gseaResult")
if (inherits(x, "gseaResult")) {
x@result$Count <- x$core_enrichment %>%
strsplit(split = "/") %>%
vapply(length, FUN.VALUE = 1)
}
n <- update_n(x, showCategory)
if (is.numeric(n)) {
keep <- seq_len(n)
} else {
keep <- match(n, rownames(x@termsim))
}
if (length(keep) == 0) {
stop("no enriched term found...")
}
## Fill the upper triangular matrix completely
termsim2 <- fill_termsim(x, keep)
## Use the ward.D method to avoid overlapping ancestor nodes of each group
hc <- stats::hclust(stats::as.dist(1- termsim2),
method = hclust_method)
clus <- stats::cutree(hc, nCluster)
d <- data.frame(label = names(clus),
#node = seq_len(length(clus)),
color = x[keep, as.character(color)],
count = x$Count[keep])
## Group the nodes.
p <- group_tree(hc = hc, clus = clus, d = d, offset_tiplab = offset_tiplab,
nWords = nWords, label_format_cladelab = label_format_cladelab,
label_format_tiplab = label_format_tiplab, offset = offset,
fontsize = fontsize, group_color = group_color, extend = extend,
hilight = hilight, cex_category = cex_category, align = align, align_tiplab = FALSE,
color = color)
# xlim <- c(0, xlim * 3 * max(p$data$x))
# p + coord_cartesian(xlim = xlim) +
# p + ggnewscale::new_scale_colour() +
# geom_tippoint(aes(color = color, size = count)) +
p + scale_size_continuous(name = "number of genes",
range = c(3, 8) * cex_category) +
ggtree::hexpand(ratio = hexpand) +
guides(size = guide_legend(order = 1),
color = guide_colorbar(order = 2))
}
##' @rdname treeplot
##' @param split Separate result by 'category' variable.
##' @param legend_n Number of circle in legend, the default value is 3.
##' Will be removed in the next version.
##' @param geneClusterPanel one of "heatMap"(default), "dotplot", "pie".
##' Will be removed in the next version.
##' @param pie Used only when geneClusterPanel = "pie",
##' proportion of clusters in the pie chart, one of 'equal' (default) and 'Count'.
##' Will be removed in the next version.
##' @param clusterPanel.params list, the parameters to control the attributes of cluster panel.
##' see the clusterPanel.params in the following.
##' clusterPanel.params control the attributes of cluster panel, it can be referred to the following parameters:
##' \itemize{
##' \item \code{clusterPanel} one of "heatMap"(default), "dotplot", "pie".
##' \item \code{pie} pUsed only when ClusterPanel = "pie",
##' proportion of clusters in the pie chart, one of 'equal' (default) and 'Count'.
##' \item \code{legend_n} number of circle in legend.
##' \item \code{colnames_angle} set the angle of colnames.
##' }
##' @importFrom ggtree nodepie
##' @importFrom ggtree geom_inset
##' @importFrom ggplot2 scale_fill_manual
##' @importFrom rlang check_installed
treeplot.compareClusterResult <- function(x,
showCategory = 5,
color = "p.adjust",
nWords = 4, # removed
nCluster = 5, # removed
cex_category = 1,
split = NULL,
label_format = NULL,
label_format_cladelab = 30, # removed
label_format_tiplab = NULL,
fontsize = 4,
offset = rel(1), # removed
pie = "equal", # removed
legend_n = 3, # removed
offset_tiplab = rel(1), # removed
hclust_method = "ward.D", # removed
group_color = NULL, # removed
extend = 0.3, # removed
hilight = TRUE, # removed
geneClusterPanel = "heatMap", # removed
hexpand = .1, # removed
align = "both", # removed
cluster.params = list(
method = "ward.D",
n = 5,
color = NULL,
label_words_n = 4,
label_format = 30
),
hilight.params = list(
hilight = TRUE,
align = "both"
),
clusterPanel.params = list(
clusterPanel = "heatMap",
pie = "equal",
legend_n = 3,
colnames_angle = 0
),
offset.params = list(
bar_tree = rel(1),
tiplab = rel(1),
extend = 0.3,
hexpand = .1
),...) {
# change parameter name
##############################################################
params_df <- as.data.frame(rbind(
c("hclust_method", "cluster.params", "method"),
c("nCluster", "cluster.params", "n"),
c("group_color", "cluster.params", "color"),
c("nWords", "cluster.params", "label_words_n"),
c("label_format_cladelab", "cluster.params", "label_format"),
c("hilight", "hilight.params", "hilight"),
c("align", "hilight.params", "align"),
c("geneClusterPanel", "clusterPanel.params", "clusterPanel"),
c("pie", "clusterPanel.params", "pie"),
c("legend_n", "clusterPanel.params", "legend_n"),
c("offset", "offset.params", "bar_tree"),
c("offset_tiplab", "offset.params", "tiplab"),
c("extend", "offset.params", "extend"),
c("hexpand", "offset.params", "hexpand"))
)
colnames(params_df) <- c("original", "listname", "present")
rownames(params_df) <- params_df$original
default.cluster.params <- list(
method = "ward.D",
n = 5,
color = NULL,
label_words_n = 4,
label_format = 30
)
default.hilight.params <- list(
hilight = TRUE,
align = "both"
)
default.clusterPanel.params <- list(
clusterPanel = "heatMap",
pie = "equal",
legend_n = 3,
colnames_angle = 0
)
default.offset.params <- list(
bar_tree = rel(1),
tiplab = rel(1),
extend = 0.3,
hexpand = .1
)
# use modifyList to change the values of parameter
cluster.params <- modifyList(default.cluster.params, cluster.params)
hilight.params <- modifyList(default.hilight.params, hilight.params)
clusterPanel.params <- modifyList(default.clusterPanel.params, clusterPanel.params)
offset.params <- modifyList(default.offset.params, offset.params)
params_list <- list(x = x,
showCategory = showCategory,
color = color,
nWords = nWords,
nCluster = nCluster,
cex_category = cex_category,
split = split,
label_format = label_format,
label_format_cladelab = label_format_cladelab,
label_format_tiplab = label_format_tiplab,
fontsize = fontsize,
offset = offset,
pie = pie,
legend_n = legend_n,
offset_tiplab = offset_tiplab,
hclust_method = hclust_method,
group_color = group_color,
extend = extend,
hilight = hilight,
geneClusterPanel = geneClusterPanel,
hexpand = hexpand,
align = align,
cluster.params = cluster.params,
hilight.params = hilight.params,
clusterPanel.params = clusterPanel.params,
offset.params = offset.params
)
# get all parameters value
args <- as.list(match.call())
removed_params <- intersect(params_df$original, names(args))
if (length(removed_params) > 0) {
for (i in removed_params) {
params_list[[params_df[i, 2]]][[params_df[i, 3]]] <- get(i)
warn <- get_param_change_message(i, params_df)
warning(warn)
}
}
cluster.params <- params_list[["cluster.params"]]
hilight.params <- params_list[["hilight.params"]]
clusterPanel.params <- params_list[["clusterPanel.params"]]
offset.params <- params_list[["offset.params"]]
hclust_method <- cluster.params[["method"]]
nCluster <- cluster.params[["n"]]
group_color <- cluster.params[["color"]]
nWords <- cluster.params[["label_words_n"]]
label_format_cladelab <- cluster.params[["label_format"]]
hilight <- hilight.params[["hilight"]]
align <- hilight.params[["align"]]
geneClusterPanel <- clusterPanel.params[["clusterPanel"]]
pie <- clusterPanel.params[["pie"]]
legend_n <- clusterPanel.params[["legend_n"]]
colnames_angle <- clusterPanel.params[["colnames_angle"]]
hilight <- hilight.params[["hilight"]]
align <- hilight.params[["align"]]
offset <- offset.params[["bar_tree"]]
offset_tiplab <- offset.params[["tiplab"]]
extend <- offset.params[["extend"]]
hexpand <- offset.params[["hexpand"]]
# geneClusterPanel <- match.arg(geneClusterPanel, c("heatMap", "dotplot", "pie"))
has_pairsim(x)
group <- Description <- Cluster <- Count <- NULL
# to compatible with older versions
if (!is.null(label_format)) {
label_format_cladelab <- label_format
}
# y <- get_selected_category(showCategory, x, split)
y <- fortify(x, showCategory = showCategory,
includeAll = TRUE, split = split)
y$Cluster <- sub("\n.*", "", y$Cluster)
if ("core_enrichment" %in% colnames(y)) { ## for GSEA result
y$geneID <- y$core_enrichment
}
## Data structure transformation, combining the same ID (Description) genes
merged_ggData <- merge_compareClusterResult(y)
ID_Cluster_mat <- prepare_pie_category(y, pie=pie)
## Fill the upper triangular matrix completely
termsim2 <- fill_termsim(x, rownames(ID_Cluster_mat))
hc <- stats::hclust(stats::as.dist(1- termsim2),
method = hclust_method)
clus <- stats::cutree(hc, nCluster)
rownames(merged_ggData) <- merged_ggData$Description
d <- data.frame(label = names(clus),
count = merged_ggData[names(clus), "Count"])
p <- group_tree(hc = hc, clus = clus, d = d, offset_tiplab = offset_tiplab,
nWords = nWords, label_format_cladelab = label_format_cladelab,
label_format_tiplab = label_format_tiplab, offset = offset,
fontsize = fontsize, group_color = group_color, extend = extend,
hilight = hilight, cex_category = cex_category, ID_Cluster_mat = ID_Cluster_mat,
geneClusterPanel = geneClusterPanel, align = align, add_tippoint = FALSE,
align_tiplab = TRUE, color = color)
p_data <- as.data.frame(p$data)
p_data <- p_data[which(!is.na(p_data$label)), ]
rownames(p_data) <- p_data$label
p_data <- p_data[rownames(ID_Cluster_mat), ]
# if (geneClusterPanel == "pie") {
# xlim <- c(0, xlim * 3 * p_data$x[1])
# } else {
# xlim <- c(0, xlim * 4.5 * p_data$x[1])
# }
if (geneClusterPanel == "pie") {
ID_Cluster_mat$radius <- sqrt(p_data$count / sum(p_data$count) * cex_category)
ID_Cluster_mat$x <- p_data$x
ID_Cluster_mat$y <- p_data$y
ID_Cluster_mat$node <- p_data$node
p <- p + ggnewscale::new_scale_fill() +
scatterpie::geom_scatterpie(aes_(x=~x,y=~y,r=~radius), data=ID_Cluster_mat,
cols=colnames(ID_Cluster_mat)[1:(ncol(ID_Cluster_mat)-4)],color=NA) +
scatterpie::geom_scatterpie_legend(ID_Cluster_mat$radius,
x = 0.8, y = 0.1, n = legend_n,
labeller = function(x) round(sum(p_data$count) * x^2 / cex_category)) +
# coord_equal(xlim = xlim) +
labs(fill = "Cluster") + coord_equal()
}
if (geneClusterPanel == "heatMap") {
heatMapData <- as.data.frame(x)
heatMapData$Cluster <- as.character(heatMapData$Cluster)
heatMapData <- heatMapData[heatMapData$Cluster %in% colnames(ID_Cluster_mat), ]
heatMapData <- heatMapData[heatMapData$Description %in% rownames(ID_Cluster_mat), ]
for (i in seq_len(nrow(heatMapData))) {
ID_Cluster_mat[heatMapData[i, "Description"], heatMapData[i, "Cluster"]] <- heatMapData[i, color]
}
p <- p + ggnewscale::new_scale_fill() # +
# coord_equal(xlim = xlim)
p <- ggtree::gheatmap(p, ID_Cluster_mat, colnames_angle = colnames_angle) +
# scale_fill_continuous(trans = "log10", name = color) +
set_enrichplot_color(type = "fill", trans = "log10", name = color)
}
if (geneClusterPanel == "dotplot") {
dotdata <- as.data.frame(x)
pData <- as.data.frame(p$data)
paths <- pData$label[order(pData$y, decreasing = TRUE)] %>% .[!is.na(.)]
dotdata <- dotdata[dotdata$Description %in% paths, ]
dotdata <- dplyr::select(dotdata, Description, dplyr::everything())
check_installed("ggtreeExtra", "for `treeplot()` with ` clusterPanel = 'dotplot'`.")
p <- p + ggnewscale::new_scale_colour() +
ggtreeExtra::geom_fruit(data = dotdata, geom = geom_point,
mapping = aes_string(x = "Cluster", y = "Description",
size = "Count", color = color),
# pwidth = 0.5, offset = -0.2,
pwidth = 0.06*ncol(ID_Cluster_mat),
axis.params = list(axis = "x", text.size = 3, line.alpha = 0, text.angle = colnames_angle)) +
# scale_colour_continuous(trans = "log10", name = color) +
set_enrichplot_color(trans = "log10", name = color)
}
p + ggtree::hexpand(ratio = hexpand)
}
##' Fill the upper triangular matrix completely
##'
##' @param x enrichment result
##' @param keep keep value
##'
##' @return a data.frame
##' @noRd
fill_termsim <- function(x, keep) {
termsim <- x@termsim[keep, keep]
termsim[which(is.na(termsim))] <- 0
termsim2 <- termsim + t(termsim)
for ( i in seq_len(nrow(termsim2)))
termsim2[i, i] <- 1
return(termsim2)
}
##' Add geom_cladelab() to a ggtree object.
##'
##' @param p a ggtree object
##' @param nWords the number of words in the cluster tags
##' @param label_format a numeric value sets wrap length, alternatively a
##' custom function to format axis labels.
##' @param offset offset of bar and text from the clade.
##' @importFrom rlang check_installed
##'
##' @return a ggtree object
##' @noRd
add_cladelab <- function(p, nWords, label_format_cladelab,
offset, roots,
fontsize, group_color, cluster_color,
pdata, extend, hilight, align) {
# align <- getOption("enriplot.treeplot.align", default = "both")
cluster_label <- sapply(cluster_color, get_wordcloud, ggData = pdata,
nWords = nWords)
label_func_cladelab <- default_labeller(label_format_cladelab)
if (is.function(label_format_cladelab)) {
label_func_cladelab <- label_format_cladelab
}
cluster_label <- label_func_cladelab(cluster_label)
n_color <- length(levels(cluster_color)) - length(cluster_color)
if (is.null(group_color)) {
check_installed('scales', 'for `add_cladelab()`.')
color2 <- scales::hue_pal()(length(roots) + n_color)
if (n_color > 0) color2 <- color2[-seq_len(n_color)]
} else {
color2 <- group_color
}
df <- data.frame(node = as.numeric(roots),
labels = cluster_label,
cluster=cluster_color,
# color = scales::hue_pal()(length(roots) + n_color)[-seq_len(n_color)]
color = color2
)
p <- p + ggnewscale::new_scale_colour() +
geom_cladelab(
data = df,
mapping = aes_(node =~ node, label =~ labels, color =~ cluster),
textcolor = "black",
extend = extend,
show.legend = FALSE,
fontsize = fontsize, offset = offset) +
scale_color_manual(values = df$color,
guide = 'none')
if (hilight) {
p <- p + ggtree::geom_hilight(
data = df,
mapping = aes_(node =~ node, fill =~ cluster),
show.legend = FALSE,
align = align) +
scale_fill_manual(values = df$color,
guide = 'none')
}
return(p)
}
##' Group the nodes.
##'
##' @return a ggtree object
##' @noRd
group_tree <- function(hc, clus, d, offset_tiplab, nWords,
label_format_cladelab, label_format_tiplab,
offset, fontsize, group_color,
extend, hilight, cex_category,
ID_Cluster_mat = NULL, geneClusterPanel = NULL,
align, add_tippoint = TRUE, align_tiplab = TRUE, color) {
group <- count <- NULL
# cluster data
dat <- data.frame(name = names(clus), cls=paste0("cluster_", as.numeric(clus)))
grp <- apply(table(dat), 2, function(x) names(x[x == 1]))
p <- ggtree(hc, hang=-1, branch.length = "none", show.legend=FALSE)
# extract the most recent common ancestor
noids <- lapply(grp, function(x) unlist(lapply(x, function(i) ggtree::nodeid(p, i))))
roots <- unlist(lapply(noids, function(x) ggtree::MRCA(p, x)))
# cluster data
p <- ggtree::groupOTU(p, grp, "group") + aes_(color =~ group)
rangeX <- max(p$data$x, na.rm=TRUE) - min(p$data$x, na.rm=TRUE)
if (inherits(offset_tiplab, "rel")) {
offset_tiplab <- unclass(offset_tiplab)
if (geneClusterPanel == "pie" || is.null(geneClusterPanel)) {
## 1.5 * max(radius_of_pie)
offset_tiplab <- offset_tiplab * .5 * max(sqrt(d$count / sum(d$count) * cex_category))
} else if (geneClusterPanel == "heatMap") {
## Close to the width of the tree
offset_tiplab <- offset_tiplab * 0.2 * ncol(ID_Cluster_mat) * rangeX
} else if (geneClusterPanel == "dotplot") {
## Close to the width of the tree
offset_tiplab <- offset_tiplab * 0.09 * ncol(ID_Cluster_mat) * rangeX
}
}
if (inherits(offset, "rel")) {
offset <- unclass(offset)
offset <- offset * rangeX * 1.2 + offset_tiplab
}
# max_nchar <- max(nchar(p$data$label), na.rm = TRUE)
pdata <- data.frame(name = p$data$label, color2 = p$data$group)
pdata <- pdata[!is.na(pdata$name), ]
cluster_color <- unique(pdata$color2)
n_color <- length(levels(cluster_color)) - length(cluster_color)
if (!is.null(group_color)) {
color2 <- c(rep("black", n_color), group_color)
p <- p + scale_color_manual(values = color2, guide = 'none')
}
p <- p %<+% d
if (!is.null(label_format_tiplab)) {
label_func_tiplab <- default_labeller(label_format_tiplab)
if (is.function(label_format_tiplab)) {
label_func_tiplab <- label_format_tiplab
}
isTip <- p$data$isTip
p$data$label[isTip] <- label_func_tiplab(p$data$label[isTip])
}
p <- add_cladelab(p = p, nWords = nWords,
label_format_cladelab = label_format_cladelab,
offset = offset, roots = roots, fontsize = fontsize,
group_color = group_color, cluster_color = cluster_color,
pdata = pdata, extend = extend, hilight = hilight, align = align)
if (add_tippoint) {
p <- p + ggnewscale::new_scale_colour() +
geom_tippoint(aes(color = color, size = count)) +
# scale_colour_continuous(name = color)+
set_enrichplot_color(name = color)
}
## add tiplab
p <- p + geom_tiplab(offset = offset_tiplab, hjust = 0,
show.legend = FALSE, align = align_tiplab, linesize = 0)
return(p)
}
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