plot.gosummaries: Plot the GOsummaries figure

Description Usage Arguments Details Value Author(s) Examples

Description

The function to draw a GOsummaries figure based on a gosummaries object. The GOsummaries figure consists of several components each defined by a gene list ora a pair of them. The GO annotations of them are shown as wordclouds. Optionally one can draw related (expression) data on panels atop of the wordclouds.

Usage

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## S3 method for class 'gosummaries'
plot(x, components = 1:min(10, length(x)),
  classes = NA, panel_plot = NULL, panel_customize = NULL,
  panel_par = list(), panel_height = 5, panel_width = 30, fontsize = 10,
  term_length = 35, wordcloud_colors = c("grey70", "grey10"),
  wordcloud_legend_title = NULL, filename = NA, ...)

Arguments

x

a gosummaries object

components

index for the components to draw.

classes

name of the variable from annotation data.frame that defines the colors in the plot

panel_plot

plotting function for panel

panel_customize

customization function for the panel plot, menat for making small changes like changing colour scheme

panel_par

list of arguments passed on to panel_plot function

panel_height

panel height as number of lines, with given fontsize. If set to 0 no panel is drawn.

panel_width

panel width in lines of text

fontsize

font size used throughout the figure in points

term_length

maximum length of the dispalyed GO categories in characters, longer names are cropped to this size

wordcloud_colors

two element vector of colors to define color scheme for displaying the enrichment p-values across the wordclouds. First element defines the color for category with worst p-value and the second for the word with the best. Set the same value for both if you want to remove the color scale and the legend.

wordcloud_legend_title

title of wordcloud legend

filename

file path where to save the picture. Filetype is decided by the extension in the path. Currently following formats are supported: png, pdf, tiff, bmp, jpeg. Even if the plot does not fit into the plotting window, the file size is calculated so that the plot would fit there.

...

not used

Details

In most cases the function can decide which type of plot to draw into the panel part. If there is no data explicitly put into the Data slots of the gosummaries object, it just draws a horizontal barplot with the numbers of genes. On visualizing the PCA data it draws histogram of the samples on the principal axes. For clustering and differential expression it draws the boxplot of expression values.

Value

The gtable object containing the figure

Author(s)

Raivo Kolde <[email protected]>

Examples

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## Not run: 
data(gs_limma)

# Default plot
plot(gs_limma, fontsize = 8)

# Omitting the panel area 
plot(gs_limma, panel_height = 0, fontsize = 8)

# Selecting only certain components
plot(gs_limma, components = c(1, 3), fontsize = 8)

# Cutting the longer terms shorter (see right wordcloud on first component)
plot(gs_limma, term_length = 20, fontsize = 8) 

# Change wordcloud colors
plot(gs_limma, term_length = 20, wordcloud_colors = c("#C6DBEF", "#08306B"), 
     fontsize = 8)

# Adjust panel plot type (see panel_boxplot help for options)
data(gs_kmeans)

plot(gs_kmeans, panel_plot = panel_violin, classes = "Tissue", components = 
     1:2, fontsize = 8)
plot(gs_kmeans, panel_plot = panel_violin_box, classes = "Tissue", 
     components = 1:2, fontsize = 8)

# Adjust colorscheme for plot (see customize help for more information) 
cust = function(p, par){
  p = p + scale_fill_brewer(par$classes, type = "qual", palette = 2)
  return(p)
}
plot(gs_kmeans, panel_plot = panel_violin, panel_customize = cust, 
     classes = "Tissue", components = 1:2, fontsize = 8)

## End(Not run)

GOsummaries documentation built on May 6, 2019, 3:52 a.m.