plot_scatter: Sample to sample scatter plot
In pachterlab/zika: Tools for investigating RNA-Seq

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

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)

`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' 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