hapVsPheno: hapVsPheno

In geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization

hapVsPheno

Description

hapVsPheno

Usage

hapVsPheno(
  hap,
  pheno,
  phenoName,
  hapPrefix = "H",
  title = "",
  comparisons = comparisons,
  method = "t.test",
  method.args = list(),
  symnum.args = list(),
  mergeFigs = FALSE,
  angle = angle,
  hjust = hjust,
  vjust = vjust,
  minAcc = minAcc,
  freq.min = freq.min,
  outlier.rm = TRUE,
  ...
)

Arguments

hap	object of hapResult class, generate withvcf2hap() or seqs2hap()
pheno	object of data.frame class, imported by import_pheno()
phenoName	pheno name for plot, should be one column name of pheno
hapPrefix	prefix of hapotypes, default as "H"
title	a charater which will used for figure title
comparisons	a list contains comparison pairs eg. list(c("H001", "H002"), c("H001", "H004")), or a character vector contains haplotype names for comparison, or "none" indicates do not add comparisons.
method	a character string indicating which method to be used for comparing means.
method.args	a list of additional arguments used for the test method. For example one might use method.args = list(alternative = "greater") for wilcoxon test.
symnum.args	a list of arguments to pass to the function symnum for symbolic number coding of p-values. For example, symnum.args <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, Inf), symbols = c("****", "***", "**", "*", "ns")). In other words, we use the following convention for symbols indicating statistical significance: ns: p > 0.05 *: p <= 0.05 **: p <= 0.01 ***: p <= 0.001 ****: p <= 0.0001
mergeFigs	bool type, indicate whether merge the heat map and box plot or not. Default as FALSE
angle	the angle of x labels
hjust, vjust	hjust and vjust of x labels
minAcc, freq.min	If observations number of a Hap less than this number will not be compared with others or be ploted. Should not less than 3 due to the t-test will meaninglessly. Default as 5
outlier.rm	whether remove ouliers, default as TRUE
...	Arguments passed on to ggpubr::ggviolin data a data frame x character string containing the name of x variable. y character vector containing one or more variables to plot combine logical value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, create a multi-panel plot by combining the plot of y variables. merge logical or character value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, merge multiple y variables in the same plotting area. Allowed values include also "asis" (TRUE) and "flip". If merge = "flip", then y variables are used as x tick labels and the x variable is used as grouping variable. color outline color. fill fill color. palette the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty". alpha color transparency. Values should be between 0 and 1. xlab character vector specifying x axis labels. Use xlab = FALSE to hide xlab. ylab character vector specifying y axis labels. Use ylab = FALSE to hide ylab. facet.by character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data. panel.labs a list of one or two character vectors to modify facet panel labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ). short.panel.labs logical value. Default is TRUE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels. linetype line types. trim If TRUE (default), trim the tails of the violins to the range of the data. If FALSE, don't trim the tails. size Numeric value (e.g.: size = 1). change the size of points and outlines. width violin width. draw_quantiles If not(NULL) (default), draw horizontal lines at the given quantiles of the density estimate. select character vector specifying which items to display. remove character vector specifying which items to remove from the plot. order character vector specifying the order of items. add character vector for adding another plot element (e.g.: dot plot or error bars). Allowed values are one or the combination of: "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range"; see ?desc_statby for more details. add.params parameters (color, shape, size, fill, linetype) for the argument 'add'; e.g.: add.params = list(color = "red"). error.plot plot type used to visualize error. Allowed values are one of c("pointrange", "linerange", "crossbar", "errorbar", "upper_errorbar", "lower_errorbar", "upper_pointrange", "lower_pointrange", "upper_linerange", "lower_linerange"). Default value is "pointrange" or "errorbar". Used only when add != "none" and add contains one "mean_*" or "med_*" where "*" = sd, se, .... label the name of the column containing point labels. Can be also a character vector with length = nrow(data). font.label a list which can contain the combination of the following elements: the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of labels. For example font.label = list(size = 14, face = "bold", color ="red"). To specify only the size and the style, use font.label = list(size = 14, face = "plain"). label.select can be of two formats: a character vector specifying some labels to show. a list containing one or the combination of the following components: top.up and top.down: to display the labels of the top up/down points. For example, label.select = list(top.up = 10, top.down = 4). criteria: to filter, for example, by x and y variabes values, use this: label.select = list(criteria = "`y` > 2 & `y` < 5 & `x` %in% c('A', 'B')"). repel a logical value, whether to use ggrepel to avoid overplotting text labels or not. label.rectangle logical value. If TRUE, add rectangle underneath the text, making it easier to read. position Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment. ggtheme function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

Value

list. A list contains a character vector with Haps were applied student test, a mattrix contains p-value of each compare of Haps and a ggplot2 object named as figs if mergeFigs set as TRUE, or two ggplot2 objects names as fig_pvalue and fig_Violin

Examples

data("geneHapR_test")
# plot the figs directly
hapVsPheno(hap = hapResult,
           pheno = pheno,
           phenoName = "GrainWeight.2021",
           minAcc = 3)

# do not merge the files
results <- hapVsPheno(hap = hapResult,
                      pheno = pheno,
                      phenoName = "GrainWeight.2021",
                      minAcc = 3,
                      mergeFigs = FALSE)
plot(results$fig_pvalue)
plot(results$fig_Violin)

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