[r] Add examples for single cell plots and trackplots#233
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Co-authored-by: Ben Parks <bnprks@users.noreply.github.com>
delete intermediates when exiting clean up docs wording
…ecessary parameterization + fix example styling
| #' @return By default, returns a ggplot2 object with all the requested features plotted | ||
| #' in a grid. If `return_data` or `return_plot_list` is called, the return value will | ||
| #' match that argument. | ||
| #' @examples |
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I'm rendering two plots, once by just the clusters, and one with the features. Not really understanding why this is erroring out, when running this code in console runs completely fine.
| #' mat_norm <- log1p(multiply_cols(mat, 1/colSums(mat)) * 10000) %>% write_matrix_memory(compress = FALSE) | ||
| #' ## Get variable genes | ||
| #' stats <- matrix_stats(mat, row_stats = "variance") | ||
| #' variable_genes <- order(stats$row_stats["variance",], decreasing=TRUE) %>% |
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Not really liking doing all of this setup where I'm doing PCA and clustering. I think this can be vastly shortened when we have the #189 feature added in + a PCA DimReduction. But should we just do it with a fake matrix created by manually concatting multiple different distributions?
| #' mat <- get_demo_mat() | ||
| #' cell_types <- paste("Group", rep(1:3, length.out = length(colnames(mat)))) | ||
| #' | ||
| #' ## Plot dot |
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Same issue with the y label where it's not being rendered properly. I think it is again with the argument_name() navigating up the call stack.
| #' @param label_size size for transcript labels in units of mm | ||
| #' @return Plot of gene locations | ||
| #' @seealso `trackplot_combine()`, `trackplot_coverage()`, `trackplot_loop()`, `trackplot_scalebar()` | ||
| #' @examples |
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Side thought but maybe it would be good to split into to y-axis levels even when there isn't direct intersection of two genes. It is a little bit hard to distinguish the genes in this example.
| #' the text label, y-axis, and plot body. The relative height of each row is given | ||
| #' by heights. A shared title and x-axis are put at the top. | ||
| #' @seealso `trackplot_coverage()`, `trackplot_gene()`, `trackplot_loop()`, `trackplot_scalebar()` | ||
| #' @examples |
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Should we expand the trackplot_combine() section, or is this good for now?
| #' @param show_strand If TRUE, show strand direction as arrows | ||
| #' @return Plot of genomic loci if return_data is FALSE, otherwise returns the data frame used to generate the plot | ||
| #' @seealso `trackplot_combine()`, `trackplot_coverage()`, `trackplot_loop()`, `trackplot_scalebar()`, `trackplot_gene()` | ||
| #' @examples |
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The peaks here don't look great, should I use a different example?
…rackplot_loop()`
immanuelazn
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This PR provides function examples for most of the functions in the
Single Cell plotsandGenomic track plotssection.This PR also provides a function (
render_plot_from_storage()) that allows for resizing plots in an example, as pkgdown does not natively provide configuration on that end.Missing functions include the following:
plot_tf_footprint()set_trackplot_label()set_trackplot_height()andget_trackplot_height().trackplot_combine()function. This would turn into an entire mini-vignette with customizing thetrackplot_combine()plot. Should this be the goal?There are some various thoughts, and issues with the plots, that I will note directly in code. However, there is a large issue that likely comes from
argument_name()that causes the plots in pkgdown to be different than what is rendered in console. I tried with and without rendering to storage, but the issue still persists.