NEWS.md

In YTLogos/ggpubr: 'ggplot2' Based Publication Ready Plots

ggpubr 0.1.5.999

New features

• New argument lab.nb.digits in ggbarplot(). Integer indicating the number of decimal places (round) to be used (#28). Example: lab.nb.digits = 2.

• New argument tip.length in stat_compare_means(). Numeric vector with the fraction of total height that the bar goes down to indicate the precise column. Default is 0.03. Can be of same length as the number of comparisons to adjust specifically the tip lenth of each comparison. For example tip.length = c(0.01, 0.03).

Major changes

Minor changes

Bug fixes

• stat_compare_means() now reacts to label = "p.format" when comparisons specified (#28).
• Now, the p.values are displayed correctly when ref.group is not the first group (@sehufnkjesktgna, #15).

ggpubr 0.1.5

Minor changes

• In ggpar(), now legend.title can be either a character vector, e.g.: legend.title = "Species" or a list, legend.title = list(color = "Species", linetype = "Species", shape = "Species").

• New argument ellipse.border.remove in ggscatter() to remove ellipse border lines.

ggscatter(mtcars, x = "mpg", y = "wt", 
          color = "cyl",
          ellipse = TRUE, mean.point = TRUE, 
          ellipse.border.remove = TRUE)

• In ggscatter(), the argument mean.point now reacts to fill color.

• Support for text justification added in ggtexttable() (@cj-wilson, #15)

• The function ggpie() can now display japanese texts. New argument font.family in ggpie() and in ggpar() (@tomochan001, #15).

• Using time on x axis works know with ggline() and ggbarplot() (@jcpsantiago, #15).

Bug fixes

• stat_compare_means() now reacts to hide.ns properly.
• drawDetails.splitText() exported so that the function ggparagraph() works properly.
• Now, ggpubr functions accept expression for label text
• In ggbarplot(), now labels correspond to the true size of bars (@tdelhomme, #15).
• stat_compare_means() now keep the default order of factor levels (@RoKant, #12).

ggpubr 0.1.4

New features

• New helper functions:

  • gradient_color() and gradient_color(): change gradient color and fill palettes.
  • clean_theme(): remove axis lines, ticks, texts and titles.
  • get_legend(): to extract the legend labels from a ggplot object.
  • as_ggplot(): Transform the output of gridExtra::arrangeGrob() and gridExtra::grid.arrange() to a an object of class ggplot.
  • ggtexttable(): to draw a textual table.
  • ggparagraph(): to draw a paragraph of text.
  • fill_palette() and color_palette() to change the fill and color palette, respectively.
  • annotate_figure() to annotate (arranged) ggplots.
  • text_grob() to create easily a customized text graphical object.
  • background_image() to add a background image to a ggplot.

• New theme function theme_transparent() to create a ggplot with transparent background.

Minor changes

• In gghistogram(), density curve and rug react to the fill color.
• ggarrange():
  • New argument àlign to specify whether graphs in the grid should be horizontally ("h") or vertically ("v") aligned.
  • New argument legend to remove or specify the legend position when arranging multiple plots.
  • New argument common.legend to create a common unique legend for multiple plots.

ggpubr 0.1.3

New features

• New functions:

  • ggarrange() to arrange multiple ggplots on the same page.
  • ggexport() to export one or multiple ggplots to a file (pdf, eps, png, jpeg).
  • ggpaired() to plot paired data.
  • compare_means() to compare the means of two or multiple groups. Returns a data frame.
  • stat_compare_means() to add p-values and significance levels to plots.
  • stat_cor() to add correlation coefficients with p-values to a scatter plot.
  • stat_stars() to add stars to a scatter plot.

• Now, the argument y can be a character vector of multiple variables to plot at once. This might be useful in genomic fields to plot the gene expression levels of multiple genes at once. see ggboxplot(), ggdotplot(), ggstripchart(), ggviolin(), ggbarplot() and ggline.

• The argument x can be a vector of multiple variables in gghistogram(), ggdensity(), ggecdf() and ggqqplot().

• New functions to edit ggplot graphical parameters:

  • font() to change the appearance of titles and labels.
  • rotate_x_text() and rotate_y_text() to rotate x and y axis texts.
  • rotate() to rotate a ggplot for creating horizontal plot.
  • set_palette() or change_palette() to change a ggplot color palette.
  • border() to add/change border lines around a ggplot.
  • bgcolor() to change ggplot panel background color.
  • rremove() to remove a specific component from a ggplot.
  • grids() to add grid lines.
  • xscale() and yscale() to change axis scale.

• New helper functions:

  • facet() added to create multi-panel plots (#5).
  • add_summary() to add summary statistics.
  • ggadd() to add summary statistics or a geometry onto a ggplot.

• New data set added: gene_citation

• New arguments in ggpar(): x.text.angle and y.text.angle

Major changes

• New arguments in ggpubr functions, see ggboxplot(), ggdotplot(), ggstripchart(), ggviolin(), ggbarplot() and ggline:

  • combine added to combine multiple y variables on the same graph.
  • merge to merge multiple y variables in the same ploting area.
  • select to select which item to display.
  • remove to remove a specific item from a plot.
  • order to order plot items.
  • label, font.label, label.select, repel, label.rectangle to add and customize labels
  • facet.by, panel.labs and short.panel.labs: support for faceting and customization of plot panels

• New argument grouping.vars in ggtext(). Grouping variables to sort the data by, when the user wants to display the top n up/down labels.

• New arguments in theme_pubr():

  • border,
  • margin,
  • legend,
  • x.text.angle

Minor changes

• Now, the argument palette Can be also a numeric vector of length(groups); in this case a basic color palette is created using the function grDevices::palette().

Bug fixes

• Now, ggpar() reacts to palette when length(palette) = 1 and palette is a color name #3.

• ggmaplot() now handles situations, wehre there is only upregulated, or downlegulated gnes.

ggpubr 0.1.2

New features

• New function get_palette() to generate a palette of k colors from ggsci palettes, RColorbrewer palettes and custom color palettes. Useful to extend RColorBrewer and ggsci to support more colors.

Minor changes

• Now the ggpar() function can handle a list of ggplots.
• Now the default legend position is right.
• New argument show.legend.text in the ggscatter() function. Use show.legend.text = FALSE to hide text in the legend.
• New arguments title, submain, subtitle, caption, font.submain, font.subtitle, font.caption in the ggpar() function.
• New argument font.family in ggscatter().

Bug fixed

• The mean within group for ggdensity (gghistogram) are now shown if data have NA values @chunkaowang, #1

ggpubr 0.1.1

New features

• New function ggtext() for textual annotation.
• New argument star.plot in ggscatter(). A logical value. If TRUE, a star plot is generated.
• New helper function geom_exec(). A helper function used by ggpubr functions to execute any geom_xx functions in ggplot2. Useful only when you want to call a geom_xx function without carrying about the arguments to put in ggplot2::aes().
• New arguments sort.val and top in ggbarplot().
  • sort.val: a string specifying whether the value should be sorted. Allowed values are "none" (no sorting), "asc" (for ascending) or "desc" (for descending).
  • top: a numeric value specifying the number of top elements to be shown.
• New function theme_classic2() added. Classic theme with axis lines.

Minor changes

• ggboxplot(), ggviolin(), ggdotplot(), ggstripchart(), gghistogram(), ggdensity(), ggecdf() and ggqqplot() can now handle one single numeric vector.

# Example
ggboxplot(iris$Sepal.Length)

• Now, in gghistogram(), when add_density = TRUE, y scale remains = "..count..".
• Now, default theme changed to theme_classic2()
• Default point size and line size set to NULL

ggpubr 0.1.0

Plot one variable - X: Continuous

• ggdensity(): Density plot
• gghistogram(): Histogram plot
• ggecdf(): Empirical cumulative density function
• ggqqplot(): QQ plots

Plot two variables - X & Y: Discrete X and Continuous Y

• ggboxplot(): Box plot
• ggviolin(): Violin plot
• ggdotplot(): Dot plot
• ggstripchart(): Stripchart (jitter)
• ggbarplot(): Bar plot
• ggline(): Line plot
• ggerrorplot(): Error plot
• ggpie(): Pie chart
• ggdotchart(): Cleveland's dot plots

Plot two continuous variables

• ggscatter(): Scatter plot

Graphical paramters

• ggpar(): Change graphical parameters
• show_line_type(): Line types available in R
• show_point_shapes(): Point shapes available in R
• theme_pubr(): Create a publication ready theme
• labs_pubr(): Format only plot labels to a publication ready style

Genomics

• ggmaplot(): MA-plot from means and log fold changes

Data

• diff_express: Differential gene expression analysis results

Other

• desc_statby(): Descriptive statistics by groups
• stat_chull(): Plot convex hull of a set of points
• stat_conf_ellipse(): Plot confidence ellipses
• stat_mean(): Draw group mean points

YTLogos/ggpubr documentation built on May 3, 2019, 9:04 p.m.