View source: R/show_group_comparison.R
show_group_comparison | R Documentation |
Using result data from get_group_comparison, this function plots
genotypes/phenotypes comparison between signature groups using ggplot2 package and return
a list of ggplot
object contains individual and combined plots. The combined
plot is easily saved to local using cowplot::save_plot()
. Of note, default fisher
test p values are shown for categorical data and fdr values are shown for
continuous data.
show_group_comparison(
group_comparison,
xlab = "group",
ylab_co = NA,
legend_title_ca = NA,
legend_position_ca = "bottom",
set_ca_sig_yaxis = FALSE,
set_ca_custom_xlab = FALSE,
show_pvalue = TRUE,
ca_p_threshold = 0.01,
method = "wilcox.test",
p.adjust.method = "fdr",
base_size = 12,
font_size_x = 12,
text_angle_x = 30,
text_hjust_x = 0.2,
...
)
group_comparison |
a |
xlab |
lab name of x axis for all plots. if it is |
ylab_co |
lab name of y axis for plots of continuous type data. Of note,
this argument should be a character vector has same length as |
legend_title_ca |
legend title for plots of categorical type data. |
legend_position_ca |
legend position for plots of categorical type data.
Of note,
this argument should be a character vector has same length as |
set_ca_sig_yaxis |
if |
set_ca_custom_xlab |
only works when |
show_pvalue |
if |
ca_p_threshold |
a p threshold for categorical variables, default is 0.01.
A p value less than 0.01 will be shown as |
method |
a character string indicating which method to be used for comparing means. It can be 't.test', 'wilcox.test' etc.. |
p.adjust.method |
correction method, default is 'fdr'. Run |
base_size |
overall font size. |
font_size_x |
font size for x. |
text_angle_x |
text angle for x. |
text_hjust_x |
adjust x axis text |
... |
other paramters pass to |
a list
of ggplot
objects.
Shixiang Wang w_shixiang@163.com
load(system.file("extdata", "toy_copynumber_signature_by_W.RData",
package = "sigminer", mustWork = TRUE
))
# Assign samples to clusters
groups <- get_groups(sig, method = "k-means")
set.seed(1234)
groups$prob <- rnorm(10)
groups$new_group <- sample(c("1", "2", "3", "4", NA), size = nrow(groups), replace = TRUE)
# Compare groups (filter NAs for categorical coloumns)
groups.cmp <- get_group_comparison(groups[, -1],
col_group = "group",
cols_to_compare = c("prob", "new_group"),
type = c("co", "ca"), verbose = TRUE
)
# Compare groups (Set NAs of categorical columns to 'Rest')
groups.cmp2 <- get_group_comparison(groups[, -1],
col_group = "group",
cols_to_compare = c("prob", "new_group"),
type = c("co", "ca"), NAs = "Rest", verbose = TRUE
)
show_group_comparison(groups.cmp)
ggcomp <- show_group_comparison(groups.cmp2)
ggcomp$co_comb
ggcomp$ca_comb
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.