plotHapTable2: plotHapTable2

In geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization

plotHapTable2

Description

plot the hapResult in table like style using grid system. This function is under development and may not stable. Some parameters may deleted or renamed in future.

Usage

plotHapTable2(
  hapSummary,
  show_indel_size = 1,
  replaceMultiAllele = TRUE,
  angle = 0,
  show_INFO = FALSE,
  INFO_split = c(";", ",", "\\|"),
  INFO_tag = "ANN",
  geneID = NA,
  tag_field = -1,
  title = "",
  gff = NULL,
  show_chr_name = TRUE,
  Chr = NULL,
  start = NULL,
  end = NULL,
  model_rect_col = "black",
  model_rect_fill = "grey80",
  model_line_col = "black",
  model_anno_txt = NULL,
  model_anno_col = "black",
  model_anno_cex = 1,
  table_txt_col = "black",
  table_txt_cex = 1,
  model_anno_pos = c(-1, -1),
  model_anno_adj = c(0, 1),
  gene_model_height = 0.2,
  space_height = 0.1,
  table_height = NULL,
  CDS_height = 0.3,
  link_line_type = 3,
  headrows = 1,
  equal_col_width = FALSE,
  head_anno = 1,
  col_annots = 0,
  row_labels = 1,
  row_annots = 1,
  table_line_col = "white",
  annot_for_each_transcrips = TRUE,
  labels_fill = "white",
  annot_fill = "grey90",
  head_fill = NULL,
  cell_fill = NULL,
  style = gpar(fontfamily = "sans", fontface = 1, cex = 0.7),
  footbar = "",
  ...
)

Arguments

hapSummary	the hapSummary or hapResult object
show_indel_size	the Indel length longer will be replaced by "i1,i2,i3,..."
replaceMultiAllele	replace multi-allele title by 'T1,T2,...' or not
angle	the angle of number positions
show_INFO	show annotation field or not, default as FALSE
INFO_split, INFO_tag, geneID, tag_field	used to set annotation in haplotype table. And the geneID was used to fileter annotation in INFO field.
title	title of plot
gff	gff or bed annotation
show_chr_name	show chromosome name at left-top cell or not
Chr, start, end	which range should be plotted in gene model
model_rect_col, model_rect_fill, model_line_col	a string specified the color for line/rectangle in gene model
table_txt_col, table_txt_cex	controls the color and size of texts in genotype table
model_anno_pos, model_anno_adj, model_anno_cex, model_anno_col, model_anno_txt	the position (x,y), just (hjust, vjust), color, size and content of annotation text in gene model
gene_model_height, table_height, space_height	the plotting range height of gene model, table and spacer
CDS_height	a numeric vector specified the height of CDS, and the height of utr is half of that, only useful when gff is provided,
link_line_type	the type of link lines for mutations in gene model and genotype table
equal_col_width	a bool or numeric vector specified whether column with should be equal
col_annots, head_anno, headrows, row_annots, row_labels	the column or row number of annotation or labels or heads
table_line_col	the line color in genotype table
annot_for_each_transcrips	mark the strand and trancripts name for each gene modle
annot_fill, head_fill, labels_fill	the fill color of annotation, head and label row or columns
cell_fill	a color vector or function or named vector specified cell fill color
style	see help(gpar)
footbar	the foot notes
...	param not used

Examples

#
data(geneHapR_test)
plotHapTable2(hapResult)
plotHapTable2(hapResult, gff = gff)

geneHapR documentation built on May 29, 2024, 11:59 a.m.