Plots Ig usage between two groups using Fisher's Exact Test
TS_plot_IG_usage_legacy.RdDEPRACATED! Instead, use TS_plot_IG_usage() Plot the Ig usage from two groups and perform Fisher's Exact Test to find significant differences. Maximum number of groups = 2
Usage
TS_plot_IG_usage_legacy(
input_file,
sample1,
sample2,
compare_what = "IGHV",
grouping_variable = "named_clusters",
export_pdf = F,
return_only_data = F,
file_name_suffix = NULL,
custom_gene_levels = NULL,
ylim_max = NULL,
p.adj.method = "hochberg",
fill_colours = c("gray80", "gray50"),
border_colour = "black",
ggplot_theme = ggplot2::theme_classic(),
plot_width = 15,
plot_height = 5,
remove_genes_present_in_one_dataset = F,
plot_zeroes = T,
file_type = "IMGT"
)Arguments
- input_file
A dataframe (e.g. from 10X Genomics Cellranger VDJ output) that includes a grouping column.
- sample1
Grouping variable value for sample 1
- sample2
Grouping variable value for sample 2
- compare_what
Genes to compare (e.g. "IGHV", "IGKV"). Defaults to "IGHV".
- grouping_variable
Column used to group data. Defaults to "named_clusters"
- export_pdf
Logical. If TRUE, exports the plot to a PDF. Defaults to FALSE
- return_only_data
Logical. If TRUE, returns only the calculated frequencies and the test matrices. Defaults to FALSE.
- file_name_suffix
Character string. Optional suffix to be added to the exported pdf.
- custom_gene_levels
Character vector. Optional, vector used to set gene list levels.
- ylim_max
Numeric. Optional upper limit for y-axis. ggplot2 will adjust the y-axis scale to fit the data.
- p.adj.method
Method for adjust for multiple tests. Defaults to 'Hochberg'. Alternative is 'FDR'.
- fill_colours
A character vector of fill colours for the two groups. Defaults to c("grey80", "grey50").
- border_colour
Colour of bar borders. Defaults to "black".
- ggplot_theme
Optional ggplot2 theme to apply. Defaults to "theme_classic".
- plot_width
Numeric. Width of exported plot in inches. Used if 'export_pdf = TRUE'. Defaults to 15.
- plot_height
Numeric. Height of exported plot in inches. Used if 'export_pdf = TRUE'. Defaults to 5.
- remove_genes_present_in_one_dataset
Logical. If TRUE, removes genes not shared by both groups. Defaults to FALSE
- plot_zeroes
Logical. If FALSE, genes with 0 counts in one group are not plotted, resulting in a wider bar for the other group.
- file_type
Set type of file/annotation input. Defaults to "IMGT". Options are "IMGT" and "AIRR".