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Creates a HIDECAN plot

Source: R/create_hidecan_plot.R
create_hidecan_plot.Rd

Creates a HIDECAN plot from a list of filtered GWAS or DE results and/or candidate genes.

Usage

create_hidecan_plot(
  x,
  chrom_length,
  colour_genes_by_score = TRUE,
  remove_empty_chrom = FALSE,
  chroms = NULL,
  chrom_limits = NULL,
  title = NULL,
  subtitle = NULL,
  n_rows = NULL,
  n_cols = 2,
  legend_position = "bottom",
  point_size = 3,
  label_size = 3.5,
  label_padding = 0.15,
  custom_aes = NULL
)

Arguments

x

A list of GWAS_data_thr, DE_data_thr, CAN_data_thr and/or CUSTOM_data_thr produced by the apply_threshold() function. If named, the names will be appended to the y-axis labels (use ' ' as empty name in the list).

chrom_length

Tibble with columns chromosome and length, giving for each chromosome its length in bp (see combine_chrom_length() function).

colour_genes_by_score

Logical, whether to colour the genes by score (TRUE) or by log2(fold-change) (FALSE). Default value is TRUE.

remove_empty_chrom

Logical, should chromosomes with no significant markers/genes nor candidate genes be removed from the plot? Default value if FALSE.

chroms

Character vector, name of chromosomes to include in the plot. If NULL (default value), all chromosomes will be included.

chrom_limits

Integer vector of length 2, or named list where the elements are integer vectors of length 2. If vector, gives the lower and upper limit of the chromosomes (in bp) to use in the plot. If a named list, names should correspond to chromosome names. Gives for each chromosome the lower and upper limits (in bp) to use in the plot. Doesn't have to be specified for all chromosomes. Default value is NULL, i.e. no limits are applied to the chromosomes (they will be plotted in their entirety).

title

Character, title of the plot. Default value is NULL (i.e. no title will be added to the plot).

subtitle

Character, subtitle of the plot. Default value is NULL (i.e. no subtitle will be added to the plot).

n_rows

Integer, number of rows of chromosomes to create in the plot. Default value is NULL.

n_cols

Integer, number of columns of chromosomes to create in the plot. Default value is 2. Will be set to NULL if n_rows is not NULL.

legend_position

Character, position of the legend in the plot. Can be bottom (default value), top, right, left or none.

point_size

Numeric, size of the points in the plot. Default value is 3.

label_size

Numeric, size of the gene labels in the plot. Default value is 3.5 (for geom_label_repel).

label_padding

Numeric, amount of padding around gene labels in the plot, as unit or number. Default value is 0.15 (for geom_label_repel).

custom_aes

Named list of plot aesthetics for custom data types. See hidecan_aes() for information about the content of each element. Default is NULL (only needed if there are CUSTOM_data_thr objects in x or to customise the aesthetics for the default data tracks).

Value

A ggplot.

Examples

if (interactive()) {
x <- get_example_data()
y <- list("GWAS" = GWAS_data(x[["GWAS"]]),
          "DE" = DE_data(x[["DE"]]),
          "CAN" = CAN_data(x[["CAN"]]))

chrom_length <- combine_chrom_length(y)

z <- list(
  apply_threshold(y[["GWAS"]], score_thr = 4),
  apply_threshold(y[["DE"]], score_thr = 1.3, log2fc_thr = 0.5),
  apply_threshold(y[["CAN"]])
)

create_hidecan_plot(z,
                    chrom_length,
                    label_size = 2)

## Colour genes according to their fold-change
create_hidecan_plot(z,
                    chrom_length,
                    colour_genes_by_score = FALSE,
                    label_size = 2)

## Add names to the datasets
create_hidecan_plot(setNames(z, c("Genomics", "RNAseq", "My list")),
                    chrom_length,
                    colour_genes_by_score = FALSE,
                    label_size = 2)

## Add names to some of the datasets only (e.g. not for GWAS results)
create_hidecan_plot(setNames(z, c(" ", "RNAseq", "My list")),
                    chrom_length,
                    colour_genes_by_score = FALSE,
                    label_size = 2)

## Set limits on all chromosomes (to "zoom in" to the 10-20Mb region)
create_hidecan_plot(z,
                    chrom_length,
                    label_size = 2,
                    chrom_limits = c(10e6, 20e6))

## Set limits on some chromosomes only
create_hidecan_plot(z,
                    chrom_length,
                    label_size = 2,
                    chrom_limits = list("ST4.03ch00" = c(10e6, 20e6),
                                        "ST4.03ch02" = c(15e6, 25e6)))
}