CADD_MAF_Plot: CADD-MAF plot.

In masato-ogishi/plotUtility: Utility functions for R graphics

CADD-MAF plot.

Description

CADD-MAF plot.

Usage

CADD_MAF_Plot(
  df_popviz,
  df_private = NULL,
  selectedMutTypes = c(Frameshift = "frameshift", Inframe = "missense", Inframe =
    "inframe_deletion"),
  homOnly = F,
  color_by = "MutType",
  shape_by = NULL,
  facet_by = NULL,
  msc = 3.33,
  minAF = 10^-6
)

Arguments

df_popviz	A data.frame which has the following columns: HOM, AF, CADD, MutType, and optionally, MutLabel
df_private	(Optional) A data.frame which has the following columns: HOM, CADD, MutType, and MutLabel
selectedMutTypes	A named characters that will be internally used to define the factor levels.
homOnly	Logical. Whether only homozygous variants (HOM>=1) should be plotted.
color_by	A string indicating the variable name to be used for coloring.
shape_by	A string indicating the variable name to be used for formatting the shape of the points.
facet_by	A string or a pair of strings indicating the column names of variables to be used for facetting.
msc	Minimal significance cutoff. Can be identified using PopViz[http://shiva.rockefeller.edu/PopViz/].
minAF	The minimal allele frequency. Private variants will be plotted based on this number.

Examples

## Not run: 
df_popviz <- data.table::fread("PopViz_Table_PDCD1_MSC99_AR.txt", check.names=T) %>%
  dplyr::mutate(MutType=CONSEQUENCE, MutLabel=NA_character_)
df_private <- readr::read_csv("JL5657.V4.2.csv") %>%
  dplyr::filter(gene=="PDCD1"&ID=="rs373081859") %>%
  dplyr::transmute(HOM=1, AF=NA, CADD=CADD_Phred_V1.3, MutType="frameshift", MutLabel="T36Hfs*70")
plt <- CADD_MAF_Plot(
  df_popviz,
  df_private,
  selectedMutTypes=c(
   "Frameshift"="frameshift",
   "Inframe"="missense",
   "Inframe"="inframe_deletion"
  ),
  homOnly=F,
  color_by="MutType",
  facet_by="HomType",
  msc=3.3313,
  minAF=10^-6
) +
  scale_color_manual(values=c("firebrick3")) +
  scale_fill_manual(values=c("firebrick3","Medium Turquoise","dimgrey"))

## End(Not run)

masato-ogishi/plotUtility documentation built on July 27, 2023, 11:37 a.m.