Improvements to shiny and plot functions (solving several open issues) #143

warrenmcg · 2017-10-20T21:45:19Z

Here is a list of issues solved and enhancements:
#124: this was due to a mistake in how shiny and the plots handled the new sleuth object API when its obj$gene_mode was TRUE. This is now fixed:

The error reporting is clearer when the user did not use extra_bootstrap_summary — and read_bootstrap_tpm if they want to see TPM) — which are essential for use with transcript view and gene view.
There was a bug which caused the bs_quants to still have est_counts as the label when the unit was scaled_reads_per_base. This is likely what was causing the problem for users who used the options above and still had an error. This is now fixed.
These changes also addressed plot_pca fails on gene_aggregated sleuth object #126, since now the plot functions make sure that the right unit is used depending on whether the sleuth object is in transcript mode or gene mode.

In addition to the above changes, several changes were made to the transcript view and gene view to accommodate when gene_mode is TRUE:

When obj$gene_mode is TRUE, the gene view on shiny now acts similarly to the old transcript view, where you can specify a gene ID and you'll get the bootstrap plot for that gene. It correctly can handle either TPM or scaled_reads_per_base. Similar to the gene view for transcripts, you can use alternative gene identifiers.
Also, when obj$gene_mode is TRUE, transcript view is now disabled (since there is no way to access normalized transcript data without rerunning sleuth prep). I couldn't figure out how to easily hide the tab, so the tab just shows a message.

In addition to #124, there were other issues handled in this pull request:

fixed the bug found in plot_qq doesn't plot highlighted point correctly #82 for plot_qq. Thanks to @a-slide for identifying the problem!
to solve error in plot_group_density function #66, enhanced plot_group_density to handle more than one covariate, and improved the error reporting for that function.
improved the sample heat map function to address Reorder samples for heat map #67 and Improvements for sample heatmap #87. This also led to improving the transcript heatmap function, which could not handle the scaled_reads_per_base unit if the object was in gene mode:
- Both use the pheatmap package now
- Both can annotate covariates from obj$samples_to_covariates
- cluster samples in sample heat map and transcripts in transcript heat map
- the plot functions now can take additional arguments to further customize the heat maps when not done in sleuth_live.

Remaining to-dos:

~~enhance shiny to handle the extra heatmap functionality.~~

…ads_per_base'

+ Gene view adapts to whether `gene_mode` is `TRUE` or not. + Transcript view now displays a message if the sleuth object is in gene mode.

…gene mode

…en in gene mode + added 'gene_to_gene' function, analogous to 'transcripts_from_gene' function + added code to make sure the transcript version of gene viewer does not execute when in gene mode, and vice versa

…rlab#66

…iate

+ switched to pheatmap package to produce the plot + add ability to cluster the rows and columns + add ability to annotate the columns with covariates

+ add 'scaled_reads_per_base' unit so gene mode can be used with this function + add option to cluster transcripts as well as samples + add ability to use a transformation function (not just a string)

… is selected

+ add option to cluster targets for transcripts/gene heat map + add option to cluster by sample for sample heat map + add option to add annotations for all possible covariates for sample heat map

+ switch to use of pheatmap + add options to customize the color palette, with low-, medium-, and high-expression colors + add option to adjust x-axis angle, similar to sample heat map + add option to annotate covariates for the samples + add '...' option to customize the pheatmap (e.g. add transcript annotations)

…mall misc changes

warrenmcg · 2017-10-23T20:26:51Z

Additional note: I added in the sleuth_live documentation from the documentation branch. This will address issue #105.

pimentel · 2017-11-10T21:01:29Z

R/plots.R

@@ -318,7 +318,7 @@ plot_pc_variance <- function(obj,
 #' @param units either 'est_counts' ('scaled_reads_per_base' for gene_mode) or 'tpm'
 #' @param trans a string pointing to a function to use for the transformation.
 #' @param grouping a string from the columns of \code{sample_to_covariates} in
-#' the sleuth object for which to group and color by
+#' the sleuth object for which to group and color by. At this time, 


do you remember what you were going to type here?

Oh, whoops. This comment was originally going to say that "At this time, only one column can be used"; however, I implemented a version that can handle more than one column, as they exist in the table. You can revert this line back.

pimentel

awesome, thanks!

pimentel · 2017-11-10T21:17:40Z

R/sleuth.R

+#' Get the \code{target_id} of a gene using other gene identifiers
+#'
+#' @param obj a \code{sleuth} object
+#' @param test a character string denoting which beta to use


note to self: remove extra documentation here

…ments + see pull request pachterlab#143 for details on the specific changes

Pascal Sturmfels and others added 29 commits August 30, 2016 14:32

extended description and added help in heat map

4a5c963

added hepler boxes to test table and transcript view

241eac1

more updates to documentation under analyses

9b88b54

added example target_id to transcript view

3901653

clean up transcript_table #vc

2ceb10e

documentation to diagnostics #vc

7f7bfef

fixed deployment bug "so" versus "obj" #vc

f98059f

fix bug where bs_quants units for gene mode counts are now 'scaled_re…

604eae3

…ads_per_base'

Improve error reporting for plotting bootstrap summary

ea0bdc8

improve error reporting on gene view in shiny

42a2a84

improve shiny handling of gene mode:

b492a5b

+ Gene view adapts to whether `gene_mode` is `TRUE` or not. + Transcript view now displays a message if the sleuth object is in gene mode.

fix use of deprecated 'switch' when plotting bootstraps

7be22a2

fix conditional behavior of gene view tab by adding input option for …

2c11ff9

…gene mode

add option to use alternative gene identifiers when in gene viewer wh…

c8545ff

…en in gene mode + added 'gene_to_gene' function, analogous to 'transcripts_from_gene' function + added code to make sure the transcript version of gene viewer does not execute when in gene mode, and vice versa

fix tags typo that caused runtime error

ff6d6f5

adjust column widths for PCA plot to fit units box for gene mode

ac40362

fix bug from issue pachterlab#82

b662e54

improve error reporting of plot_group_density to resolve issue pachte…

a54200a

…rlab#66

enhanced plot_group_density to allow for grouping more than one covar…

5865739

…iate

improve sample heatmap function

04c4c7a

+ switched to pheatmap package to produce the plot + add ability to cluster the rows and columns + add ability to annotate the columns with covariates

improve transcript heatmap function

ac083a8

+ add 'scaled_reads_per_base' unit so gene mode can be used with this function + add option to cluster transcripts as well as samples + add ability to use a transformation function (not just a string)

add 'pheatmap' package to dependencies

e278e96

fix documentation for sample heatmap; fix bug when only one covariate…

4c1f415

… is selected

add options for both heatmaps:

297df7f

+ add option to cluster targets for transcripts/gene heat map + add option to cluster by sample for sample heat map + add option to add annotations for all possible covariates for sample heat map

remove deprecated ggPlotExpression function

b434e71

add option to annotate covariates on transcript/gene heat map; make s…

2c0deb2

…mall misc changes

add credits

34d8d08

merge in documentation from 'documentation' branch for sleuth_live

e7ab8c1

add shiny documentation to several additional components

eca4372

warrenmcg force-pushed the issue124 branch from cd171b6 to eca4372 Compare October 23, 2017 20:27

pimentel reviewed Nov 10, 2017

View reviewed changes

pimentel added 2 commits November 10, 2017 13:29

remove extra documentation

1994b70

small documentation fix

3a9c46e

pimentel approved these changes Nov 10, 2017

View reviewed changes

pimentel merged commit 96fed31 into pachterlab:devel Nov 10, 2017

warrenmcg added a commit to warrenmcg/sleuth that referenced this pull request Mar 13, 2018

reintegrate shiny documentation, gene mode changes, and shiny enhance…

9641d1d

…ments + see pull request pachterlab#143 for details on the specific changes

warrenmcg mentioned this pull request Mar 13, 2018

Shiny and Plot Fixes / Enhancements #159

Merged

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Improvements to shiny and plot functions (solving several open issues) #143

Improvements to shiny and plot functions (solving several open issues) #143

warrenmcg commented Oct 20, 2017 •

edited

Loading

warrenmcg commented Oct 23, 2017 •

edited

Loading

pimentel Nov 10, 2017

warrenmcg Nov 10, 2017

pimentel left a comment

pimentel Nov 10, 2017

Improvements to shiny and plot functions (solving several open issues) #143

Improvements to shiny and plot functions (solving several open issues) #143

Conversation

warrenmcg commented Oct 20, 2017 • edited Loading

warrenmcg commented Oct 23, 2017 • edited Loading

pimentel Nov 10, 2017

Choose a reason for hiding this comment

warrenmcg Nov 10, 2017

Choose a reason for hiding this comment

pimentel left a comment

Choose a reason for hiding this comment

pimentel Nov 10, 2017

Choose a reason for hiding this comment

warrenmcg commented Oct 20, 2017 •

edited

Loading

warrenmcg commented Oct 23, 2017 •

edited

Loading