ggbootUV | R Documentation |
Plots a sample statistic, such as the mean or median, and associated bootstrapped 95% confidence intervals for specified subsets of observations. Facilitates hypothesis testing by allowing a) application of the Benjamini-Hochberg procedure to control the alse discovery rate and b) specification of a minimum effect size.
ggbootUV(data, resp, xAxis, col = NULL, facet = NULL, nullBFactor = 10,
diff = NULL, calcStat = "mean", B = 10, seB = 200,
pMethod = "percT", fdr = 0.01, altSide, nSide = 1, ciMethod = "bca",
alpha = 0.05, minEff = 0, hLineVec = NULL, nullValue = 0,
xLab = NULL, yLab = "Response", xAxisLabVec = NULL, rotXText = FALSE,
remXAxisMarks = FALSE, pointSize = 2, errBarSize = 1,
errBarSizeRatio = 2, errBarAlpha = 0.7, errBarAlphaRatio = 2,
eqErrBarWidth = TRUE, errBarLineType = "dotted", colLabName = NULL,
colourVec = c("darkorchid1", "springgreen2", "maroon1", "dodgerblue", "red",
"yellow3", "cyan2", "orange2"), colLabVec = NULL, facetLabVec = NULL,
facetScale = "free", nCol = 2, plotTblName = NULL,
fontScaleFactor = 1, lineScaleFactor = 1, hLineFactor = 1,
bootT = TRUE, trim = 0.2, bootSECorr = FALSE)
data |
dataframe. Has one row per observation and the column names specified below. |
resp |
unquoted expression. Response variable name. |
xAxis |
unquoted expression. X-axis variable name. |
col |
unquoted expression. Colour variable name. |
facet |
unquoted expression. Facet variable name. |
diff |
unquoted expression. Difference variable name. Must be a binary variable, preferrably ('0','1') as then it is clear that the difference is the amount by which the observations labelled '1' are greater than the observations labelled '0'. |
calcStat |
function olr character. Bootstrap statistic function. Functions other than mean or median used at own risk. |
B |
integer. Number of bootstrap samples per subgroup. |
pMethod |
"perc" or "percT". Method to use for calculating p-values. Both uses the bootstrap percentile method, but "perc" does this on the mean or median, whilst "percT" does this on the t-statistic based on the mean or median. |
fdr |
numeric. False discovery rate. |
nSide |
1 or 2. Number of sides of the hypothesis tests. |
ciMethod |
"perc" or "bca". method to use to calculate confidence intervals. Both use bootstrap samples, but "perc" uses the percentile method and "bca" the bias-corrected and adjusted method. |
alpha |
numeric. 1- |
minEff |
numeric. Minimum effect size. Default is 0. |
hLineVec |
numeric vector. Heights of dashed horizontal lines to plot. Useful for indicating minimum effect size. |
nullValue |
numeric. Null hypothesis value for statistic. |
xLab, yLab |
characeter. X- and y-axis titles. Optional. |
xAxisLabVec |
named character vector. Labels for x-axis variable. Optional. |
rotXText |
logical. If TRUE, then the x-axis text is rotated 90 degrees clockwise. |
remXAxisMarks |
logical. If TRUE, then the x-axis ticks and text are removed. |
pointSize |
numeric. Size of plot points |
errBarSize |
numeric. Size of error bar |
errBarSizeRatio |
numeric. How many times larger the size is of the statistically significant error bars than the non-statistically significant bars are. |
errBarAlpha |
numeric. Error bar alpha |
errBarAlphaRatio |
numeric. How many times greater the alpha is of the statistically significant error bars than the non-statistically significant bars are. |
eqErrBarWidth |
logical. If |
colLabName |
character. Name for colour legend. Optional. |
colourVec |
character vector. Colours for colour scale. Optional. Label with factor levels to match levels to colours manually. |
colLabVec |
named character vector. Labels for colour variable. Optional. |
facetScale |
'free', 'free_x' or 'free_y'. Facet scale. |
nCol |
numeric. Number of columns to use. |
plotTblName |
character. If not NULL, then the dataframe used to plot is saved to global environment with name |
fontScaleFactor |
numeric. Factor by which to scale the text size from the default. |
lineScaleFactor |
numeric. Factor by which to scale the line size from the default. |
hLineFactor |
numeric. Factor by which to scale the horizontal line size from the default. |
altSde |
'high', 'low' or 'both'. Character specifying the alternative hypothesis relative to the null hypothesis. Note that you must still specify nSide, even if altSide is specified. |
facetlabeVec |
named character vector. Labels for facet fariable. Optional. |
sigIndType |
character vector. Must contain at least one of |
a ggplot2 object
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