plot_scatterR Documentation

Sample to sample scatter plot

Description

Make a scatter plot of transcripts from two samples. to assess correlation

Usage

plot_scatter(obj, sample_x = obj$sample_to_covariates$sample[1],
  sample_y = obj$sample_to_covariates$sample[2], use_filtered = TRUE,
  units = "est_counts", offset = 1, point_alpha = 0.2, xy_line = TRUE,
  xy_line_color = "red", trans = "log", xlim = NULL, ylim = NULL)

Arguments

obj

a sleuth object

sample_x

the string corresponding to the sample name in obj$sample_to_covariates

sample_y

same as sample_x but for the y-axis

use_filtered

if TRUE, use filtered data. otherwise, use all data

units

either 'est_counts' ('scaled_reads_per_base' for gene_mode) or 'tpm'

offset

a linear offset to help deal with zeroes if transforming the abundances

point_alpha

the alpha on the points

xy_line

if TRUE, plot the xy_line

xy_line_color

a string denoting the color for the xy line

trans

a string pointing to a function to use for the transformation. This function must exist in the global namespace. This means you should be able to call eval('myfun') and get a function back.

xlim

a numeric vector of length two denoting the x limits

ylim

same as xlim but for the y-axis

Value

a ggplot object for the scatterplot