draw_value_idr_scatterplot {idr2d} | R Documentation |
Creates diagnostic plots to visualize the results of
estimate_idr
.
draw_value_idr_scatterplot( df, remove_na = TRUE, remove_outliers = TRUE, xlab = "transformed value in replicate 1", ylab = "transformed value in replicate 2", log_axes = FALSE, log_idr = FALSE, title = "value - IDR dependence", color_gradient = c("rainbow", "default"), alpha = 1, max_points_shown = 2500 )
df |
part of output of
| ||||||
remove_na |
logical; should NA values be removed? | ||||||
remove_outliers |
logical; removes extreme data points | ||||||
xlab |
character; x axis label | ||||||
ylab |
character; y axis label | ||||||
log_axes |
logical; show logarithmized values from replicate 1 and 2 (default value is FALSE) | ||||||
log_idr |
logical; use logarithmized IDRs for colors to better distinguish highly significant IDRs (default value is FALSE) | ||||||
title |
character; plot title | ||||||
color_gradient |
character; either "rainbow" or "default" | ||||||
alpha |
numeric; transparency of dots, from 0.0 - 1.0, where 1.0 is completely opaque; default is 1.0 | ||||||
max_points_shown |
integer; default is 2500 |
ggplot2 object; IDR value scatterplot
idr_results <- estimate_idr1d(idr2d:::chipseq$rep1_df, idr2d:::chipseq$rep2_df, value_transformation = "log") draw_value_idr_scatterplot(idr_results$rep1_df)