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ggtheme also accepts objects of 'theme' type #11

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Aug 29, 2018
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ggtheme also accepts objects of 'theme' type #11

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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -20,4 +20,4 @@ Suggests:
knitr
URL: http://www.sthda.com/english/wiki/ggcorrplot
BugReports: https://github.com/kassambara/ggcorrplot/issues
RoxygenNote: 5.0.1
RoxygenNote: 6.1.0.9000
137 changes: 85 additions & 52 deletions R/ggcorrplot.R
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Expand Up @@ -7,9 +7,10 @@
#' @param method character, the visualization method of correlation matrix to be
#' used. Allowed values are "square" (default), "circle".
#' @param type character, "full" (default), "lower" or "upper" display.
#' @param ggtheme function, ggplot2 theme name. Default value is theme_minimal.
#' Allowed values are the official ggplot2 themes including theme_gray,
#' theme_bw, theme_minimal, theme_classic, theme_void, ....
#' @param ggtheme ggplot2 function or theme object. Default value is
#' `theme_minimal`. Allowed values are the official ggplot2 themes including
#' theme_gray, theme_bw, theme_minimal, theme_classic, theme_void, .... Theme
#' objects are also allowed (e.g., `theme_classic()`).
#' @param title character, title of the graph.
#' @param show.legend logical, if TRUE the legend is displayed.
#' @param legend.title a character string for the legend title. lower
Expand Down Expand Up @@ -68,63 +69,76 @@
#' # Types of correlogram layout
#' # --------------------------------
#' # Get the lower triangle
#' ggcorrplot(corr, hc.order = TRUE, type = "lower",
#' outline.col = "white")
#' ggcorrplot(corr,
#' hc.order = TRUE, type = "lower",
#' outline.col = "white"
#' )
#' # Get the upeper triangle
#' ggcorrplot(corr, hc.order = TRUE, type = "upper",
#' outline.col = "white")
#' ggcorrplot(corr,
#' hc.order = TRUE, type = "upper",
#' outline.col = "white"
#' )
#'
#' # Change colors and theme
#' # --------------------------------
#' # Argument colors
#' ggcorrplot(corr, hc.order = TRUE, type = "lower",
#' outline.col = "white",
#' ggtheme = ggplot2::theme_gray,
#' colors = c("#6D9EC1", "white", "#E46726"))
#' ggcorrplot(corr,
#' hc.order = TRUE, type = "lower",
#' outline.col = "white",
#' ggtheme = ggplot2::theme_gray,
#' colors = c("#6D9EC1", "white", "#E46726")
#' )
#'
#' # Add correlation coefficients
#' # --------------------------------
#' # argument lab = TRUE
#' ggcorrplot(corr, hc.order = TRUE, type = "lower",
#' lab = TRUE)
#' ggcorrplot(corr,
#' hc.order = TRUE, type = "lower",
#' lab = TRUE,
#' ggtheme = ggplot2::theme_dark(),
#' )
#'
#' # Add correlation significance level
#' # --------------------------------
#' # Argument p.mat
#' # Barring the no significant coefficient
#' ggcorrplot(corr, hc.order = TRUE,
#' type = "lower", p.mat = p.mat)
#' ggcorrplot(corr,
#' hc.order = TRUE,
#' type = "lower", p.mat = p.mat
#' )
#' # Leave blank on no significant coefficient
#' ggcorrplot(corr, p.mat = p.mat, hc.order = TRUE,
#' type = "lower", insig = "blank")
#'
#' ggcorrplot(corr,
#' p.mat = p.mat, hc.order = TRUE,
#' type = "lower", insig = "blank"
#' )
#' @name ggcorrplot
#' @rdname ggcorrplot
#' @export
ggcorrplot <- function (corr, method = c("square", "circle"),
type = c("full", "lower", "upper"),
ggtheme = ggplot2::theme_minimal,
title = "", show.legend = TRUE, legend.title = "Corr", show.diag = FALSE,
colors = c("blue", "white", "red"), outline.color = "gray",
hc.order = FALSE, hc.method = "complete",
lab = FALSE, lab_col = "black", lab_size = 4,
p.mat = NULL, sig.level = 0.05, insig = c("pch", "blank"),
pch = 4, pch.col = "black", pch.cex = 5,
tl.cex = 12, tl.col = "black", tl.srt = 45) {

ggcorrplot <- function(corr, method = c("square", "circle"),
type = c("full", "lower", "upper"),
ggtheme = ggplot2::theme_minimal,
title = "", show.legend = TRUE, legend.title = "Corr", show.diag = FALSE,
colors = c("blue", "white", "red"), outline.color = "gray",
hc.order = FALSE, hc.method = "complete",
lab = FALSE, lab_col = "black", lab_size = 4,
p.mat = NULL, sig.level = 0.05, insig = c("pch", "blank"),
pch = 4, pch.col = "black", pch.cex = 5,
tl.cex = 12, tl.col = "black", tl.srt = 45) {
type <- match.arg(type)
method <- match.arg(method)
insig <- match.arg(insig)

if (!is.matrix(corr) & !is.data.frame(corr))
if (!is.matrix(corr) & !is.data.frame(corr)) {
stop("Need a matrix or data frame!")
}
corr <- as.matrix(corr)

if (hc.order) {
ord <- .hc_cormat_order(corr)
corr <- corr[ord, ord]
if (!is.null(p.mat))
if (!is.null(p.mat)) {
p.mat <- p.mat[ord, ord]
}
}

# Get lower or upper triangle
Expand All @@ -145,32 +159,44 @@ ggcorrplot <- function (corr, method = c("square", "circle"),
p.mat <- reshape2::melt(p.mat, na.rm = TRUE)
corr$coef <- corr$value
corr$pvalue <- p.mat$value
corr$signif <- as.numeric(p.mat$value <= sig.level)
corr$signif <- as.numeric(p.mat$value <= sig.level)
p.mat <- subset(p.mat, p.mat$value > sig.level)
if (insig == "blank")
if (insig == "blank") {
corr$value <- corr$value * corr$signif
}
}

corr$abs_corr <- abs(corr$value) * 10

# Heatmap
p <-
ggplot2::ggplot(corr, ggplot2::aes_string("Var1", "Var2", fill = "value"))
if (method == "square")
if (method == "square") {
p <- p + ggplot2::geom_tile(color = outline.color)
else if (method == "circle") {
p <- p + ggplot2::geom_point(color = outline.color,
shape = 21, ggplot2::aes_string(size = "abs_corr")) +
} else if (method == "circle") {
p <- p + ggplot2::geom_point(
color = outline.color,
shape = 21, ggplot2::aes_string(size = "abs_corr")
) +
ggplot2::scale_size(range = c(4, 10)) + ggplot2::guides(size = FALSE)
}

p <-
p + ggplot2::scale_fill_gradient2(
low = colors[1], high = colors[3], mid = colors[2],
midpoint = 0, limit = c(-1,1), space = "Lab",
midpoint = 0, limit = c(-1, 1), space = "Lab",
name = legend.title
) +
ggtheme() +
)

# depending on the class of the object, add the specified theme
if (class(ggtheme)[[1]] == "function") {
p <- p + ggtheme()
} else if (class(ggtheme)[[1]] == "theme") {
p <- p + ggtheme
}


p <- p +
ggplot2::theme(
axis.text.x = ggplot2::element_text(
angle = tl.srt, vjust = 1, size = tl.cex, hjust = 1
Expand All @@ -180,13 +206,14 @@ ggcorrplot <- function (corr, method = c("square", "circle"),
ggplot2::coord_fixed()

label <- round(corr[, "value"], 2)
if (lab)
if (lab) {
p <- p +
ggplot2::geom_text(
ggplot2::aes_string("Var1", "Var2"),
label = label,
color = lab_col, size = lab_size
)
ggplot2::geom_text(
ggplot2::aes_string("Var1", "Var2"),
label = label,
color = lab_col, size = lab_size
)
}

if (!is.null(p.mat) & insig == "pch") {
p <- p + ggplot2::geom_point(
Expand All @@ -197,10 +224,12 @@ ggcorrplot <- function (corr, method = c("square", "circle"),
}

# Add titles
if (title != "")
if (title != "") {
p <- p + ggplot2::ggtitle(title)
if (!show.legend)
}
if (!show.legend) {
p <- p + ggplot2::theme(legend.position = "none")
}


p <- p + .no_panel()
Expand Down Expand Up @@ -239,21 +268,25 @@ cor_pmat <- function(x, ...) {

# Get lower triangle of the correlation matrix
.get_lower_tri <- function(cormat, show.diag = FALSE) {
if (is.null(cormat))
if (is.null(cormat)) {
return(cormat)
}
cormat[upper.tri(cormat)] <- NA
if (!show.diag)
if (!show.diag) {
diag(cormat) <- NA
}
return(cormat)
}

# Get upper triangle of the correlation matrix
.get_upper_tri <- function(cormat, show.diag = FALSE) {
if (is.null(cormat))
if (is.null(cormat)) {
return(cormat)
}
cormat[lower.tri(cormat)] <- NA
if (!show.diag)
if (!show.diag) {
diag(cormat) <- NA
}
return(cormat)
}

Expand Down
7 changes: 4 additions & 3 deletions ggcorrplot.Rproj
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@@ -1,8 +1,8 @@
Version: 1.0

RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default
RestoreWorkspace: No
SaveWorkspace: No
AlwaysSaveHistory: No

EnableCodeIndexing: Yes
UseSpacesForTab: Yes
Expand All @@ -18,3 +18,4 @@ StripTrailingWhitespace: Yes
BuildType: Package
PackageUseDevtools: Yes
PackageInstallArgs: --no-multiarch --with-keep.source
PackageRoxygenize: rd,collate,namespace
62 changes: 36 additions & 26 deletions man/ggcorrplot.Rd
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