plotHapTable2 {geneHapR}

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)