From d9d3a6cafec20bf50054df457a407f6d9769bf95 Mon Sep 17 00:00:00 2001
From: Chirag Parsania <chirag.parsania@gmail.com>
Date: Tue, 30 Jan 2024 16:08:45 +1100
Subject: [PATCH] bug fix

---
 R/splicewiz_wrappers.R                  |  15 +++++-
 docs/reference/Rplot001.png             | Bin 21035 -> 1011 bytes
 docs/reference/get_ASE_data_matrix.html |  61 ++++++++++++------------
 man/get_ASE_data_matrix.Rd              |  11 ++++-
 4 files changed, 53 insertions(+), 34 deletions(-)

diff --git a/R/splicewiz_wrappers.R b/R/splicewiz_wrappers.R
index 4713508..977aa36 100644
--- a/R/splicewiz_wrappers.R
+++ b/R/splicewiz_wrappers.R
@@ -201,6 +201,9 @@ get_diff_ASE_count_barplot <- function(x,
 #' @param summarise_groups_by a character string denoting a method to summaries groups. Can be one of the `mean` or `median`.
 #' @param column_condition a character string denoting a condition column from `se` to select samples. Same column will also be used to group and summaries samples.
 #' @param method a character string denoting a method for data value. Can be one of the "PSI", "logit" or "Z-Score".
+#' @param depth_threshold default 10, refer `depth_threshold` of [SpliceWiz::makeMatrix()]
+#' @param logit_max default 5, refer `logit_max` of [SpliceWiz::makeMatrix()]
+#' @param na.percent.max default 0.1, refer `na.percent.max` of [SpliceWiz::makeMatrix()]
 #'
 #' @return a data matrix
 #' @export
@@ -213,7 +216,13 @@ get_diff_ASE_count_barplot <- function(x,
 #' get_ASE_data_matrix(se, event_names , samples = c("A", "B"), column_condition ="treatment")
 #' get_ASE_data_matrix(se, event_names , samples = c("P", "Q","R"), column_condition ="replicate")
 #'
-get_ASE_data_matrix <- function(se , event_names,samples,summarise_groups=TRUE,summarise_groups_by = "mean", method ="PSI", column_condition ="condition"){
+get_ASE_data_matrix <- function(se , event_names,samples,summarise_groups=TRUE,
+                                summarise_groups_by = "mean",
+                                method ="PSI", column_condition ="condition",
+                                depth_threshold = 10,
+                                logit_max = 5,
+                                na.percent.max = 0.1
+                                ){
 
   match.arg(arg = summarise_groups_by, choices = c("mean","median"))
 
@@ -227,7 +236,9 @@ get_ASE_data_matrix <- function(se , event_names,samples,summarise_groups=TRUE,s
   data_matrix <- SpliceWiz::makeMatrix(se = se,
                                        event_list = event_names,
                                        sample_list = samples_repli$samples,
-                                       method = method) %>%
+                                       method = method,
+                                       depth_threshold=depth_threshold,logit_max =logit_max,
+                                       na.percent.max= na.percent.max) %>%
     as.data.frame() %>%
     tibble::rownames_to_column(var = "event_name") %>%
     tibble::tibble()
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
index eb05085dbd89d448de12d08baa7aaffd55a80e41..17a358060aed2a86950757bbd25c6f92c08c458f 100644
GIT binary patch
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diff --git a/docs/reference/get_ASE_data_matrix.html b/docs/reference/get_ASE_data_matrix.html
index f05b607..fa87ba5 100644
--- a/docs/reference/get_ASE_data_matrix.html
+++ b/docs/reference/get_ASE_data_matrix.html
@@ -55,7 +55,10 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span>  summarise_groups <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  summarise_groups_by <span class="op">=</span> <span class="st">"mean"</span>,</span>
 <span>  method <span class="op">=</span> <span class="st">"PSI"</span>,</span>
-<span>  column_condition <span class="op">=</span> <span class="st">"condition"</span></span>
+<span>  column_condition <span class="op">=</span> <span class="st">"condition"</span>,</span>
+<span>  depth_threshold <span class="op">=</span> <span class="fl">10</span>,</span>
+<span>  logit_max <span class="op">=</span> <span class="fl">5</span>,</span>
+<span>  na.percent.max <span class="op">=</span> <span class="fl">0.1</span></span>
 <span><span class="op">)</span></span></code></pre></div>
     </div>
 
@@ -88,6 +91,18 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 <dt>column_condition</dt>
 <dd><p>a character string denoting a condition column from <code>se</code> to select samples. Same column will also be used to group and summaries samples.</p></dd>
 
+
+<dt>depth_threshold</dt>
+<dd><p>default 10, refer <code>depth_threshold</code> of <code><a href="https://rdrr.io/pkg/SpliceWiz/man/make_plot_data.html" class="external-link">SpliceWiz::makeMatrix()</a></code></p></dd>
+
+
+<dt>logit_max</dt>
+<dd><p>default 5, refer <code>logit_max</code> of <code><a href="https://rdrr.io/pkg/SpliceWiz/man/make_plot_data.html" class="external-link">SpliceWiz::makeMatrix()</a></code></p></dd>
+
+
+<dt>na.percent.max</dt>
+<dd><p>default 0.1, refer <code>na.percent.max</code> of <code><a href="https://rdrr.io/pkg/SpliceWiz/man/make_plot_data.html" class="external-link">SpliceWiz::makeMatrix()</a></code></p></dd>
+
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
@@ -102,39 +117,23 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="fu">SpliceWiz</span><span class="fu">::</span><span class="fu">colData</span><span class="op">(</span><span class="va">se</span><span class="op">)</span><span class="op">$</span><span class="va">treatment</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A"</span>, <span class="st">"B"</span><span class="op">)</span>, each <span class="op">=</span> <span class="fl">3</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">SpliceWiz</span><span class="fu">::</span><span class="fu">colData</span><span class="op">(</span><span class="va">se</span><span class="op">)</span><span class="op">$</span><span class="va">replicate</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"P"</span>,<span class="st">"Q"</span>,<span class="st">"R"</span><span class="op">)</span>, <span class="fl">2</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">res</span> <span class="op">&lt;-</span> <span class="fu"><a href="run_ase_diff_analysis.html">run_ase_diff_analysis</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">se</span>, test_factor <span class="op">=</span> <span class="st">"treatment"</span>, test_nom <span class="op">=</span> <span class="st">"A"</span> ,test_denom <span class="op">=</span> <span class="st">"B"</span>,  IRmode <span class="op">=</span><span class="st">"annotated"</span>,  cutoff_lfc <span class="op">=</span> <span class="fl">0.6</span>, cutoff_padj <span class="op">=</span> <span class="fl">1</span>, regul_based_upon <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Mar 29 12:40:36 Performing edgeR contrast for included / excluded counts separately</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Mar 29 12:40:37 Performing edgeR contrast for included / excluded counts together</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Attaching package: ‘purrr’</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> The following object is masked from ‘package:magrittr’:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>     set_names</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Jan 30 16:07:56 Performing edgeR contrast for included / excluded counts separately</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Jan 30 16:07:58 Performing edgeR contrast for included / excluded counts together</span>
 <span class="r-in"><span><span class="va">event_names</span> <span class="op">=</span> <span class="fu"><a href="get_ASE_by_regulation.html">get_ASEsets_by_regulation</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">res</span>, sample_comparisons <span class="op">=</span> <span class="st">"A_VS_B"</span>, regul <span class="op">=</span> <span class="st">"all"</span><span class="op">)</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/r/base/unlist.html" class="external-link">unlist</a></span><span class="op">(</span><span class="op">)</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in purrr::discard(ase, ~nrow(..1) &gt; 0):</span> <span style="color: #00BBBB;">ℹ</span> In index: 1.</span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> With name: sample_comparisons.</span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Caused by error:</span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> `.p()` must return a single `TRUE` or `FALSE`, not an empty logical</span>
+<span class="r-err co"><span class="r-pr">#&gt;</span>   vector.</span>
 <span class="r-in"><span><span class="fu">get_ASE_data_matrix</span><span class="op">(</span><span class="va">se</span>, <span class="va">event_names</span> , samples <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A"</span>, <span class="st">"B"</span><span class="op">)</span>, column_condition <span class="op">=</span><span class="st">"treatment"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 99 × 3</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    event_name                                       A      B</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>                                        <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> A3SS:NSUN5-201-exon3;NSUN5-203-exon3        1      0.996 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> A3SS:NSUN5-201-exon7;NSUN5-206-exon6        0.879  0.908 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> A3SS:NSUN5-201-exon8;NSUN5-novelTr003-exon2 0.953  0.958 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> A3SS:NSUN5-204-exon10;NSUN5-202-exon10      0.955  0.941 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> A3SS:SRSF1-201-exon4;SRSF1-novelTr001-exon2 0.766  0.877 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> A3SS:SRSF1-204-exon4;SRSF1-203-exon2        0.963  0.916 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> A3SS:SRSF2-202-exon2;SRSF2-201-exon2        0.988  0.989 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> A3SS:SRSF2-206-exon2;SRSF2-202-exon3        0.165  0.159 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> A3SS:SRSF2-206-exon2;SRSF2-novelTr003-exon2 0.988  0.981 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> A3SS:SRSF2-novelTr002-exon2;SRSF2-209-exon2 0.053<span style="text-decoration: underline;">0</span> 0.059<span style="text-decoration: underline;">6</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 89 more rows</span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in event_list %in% rownames(se):</span> object 'event_names' not found</span>
 <span class="r-in"><span><span class="fu">get_ASE_data_matrix</span><span class="op">(</span><span class="va">se</span>, <span class="va">event_names</span> , samples <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"P"</span>, <span class="st">"Q"</span>,<span class="st">"R"</span><span class="op">)</span>, column_condition <span class="op">=</span><span class="st">"replicate"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 99 × 4</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    event_name                                       P       Q      R</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>                                        <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> A3SS:NSUN5-201-exon3;NSUN5-203-exon3        0.997  1       0.997 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> A3SS:NSUN5-201-exon7;NSUN5-206-exon6        0.836  0.911   0.933 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> A3SS:NSUN5-201-exon8;NSUN5-novelTr003-exon2 0.929  0.979   0.959 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> A3SS:NSUN5-204-exon10;NSUN5-202-exon10      0.954  0.957   0.933 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> A3SS:SRSF1-201-exon4;SRSF1-novelTr001-exon2 0.807  0.738   0.920 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> A3SS:SRSF1-204-exon4;SRSF1-203-exon2        0.970  0.984   0.865 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> A3SS:SRSF2-202-exon2;SRSF2-201-exon2        0.984  0.988   0.993 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> A3SS:SRSF2-206-exon2;SRSF2-202-exon3        0.158  0.219   0.110 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> A3SS:SRSF2-206-exon2;SRSF2-novelTr003-exon2 0.987  0.996   0.971 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> A3SS:SRSF2-novelTr002-exon2;SRSF2-209-exon2 0.095<span style="text-decoration: underline;">4</span> 0.008<span style="text-decoration: underline;">64</span> 0.064<span style="text-decoration: underline;">9</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 89 more rows</span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in event_list %in% rownames(se):</span> object 'event_names' not found</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/man/get_ASE_data_matrix.Rd b/man/get_ASE_data_matrix.Rd
index d5bd0fc..bb50f35 100644
--- a/man/get_ASE_data_matrix.Rd
+++ b/man/get_ASE_data_matrix.Rd
@@ -11,7 +11,10 @@ get_ASE_data_matrix(
   summarise_groups = TRUE,
   summarise_groups_by = "mean",
   method = "PSI",
-  column_condition = "condition"
+  column_condition = "condition",
+  depth_threshold = 10,
+  logit_max = 5,
+  na.percent.max = 0.1
 )
 }
 \arguments{
@@ -28,6 +31,12 @@ get_ASE_data_matrix(
 \item{method}{a character string denoting a method for data value. Can be one of the "PSI", "logit" or "Z-Score".}
 
 \item{column_condition}{a character string denoting a condition column from \code{se} to select samples. Same column will also be used to group and summaries samples.}
+
+\item{depth_threshold}{default 10, refer \code{depth_threshold} of \code{\link[SpliceWiz:make_plot_data]{SpliceWiz::makeMatrix()}}}
+
+\item{logit_max}{default 5, refer \code{logit_max} of \code{\link[SpliceWiz:make_plot_data]{SpliceWiz::makeMatrix()}}}
+
+\item{na.percent.max}{default 0.1, refer \code{na.percent.max} of \code{\link[SpliceWiz:make_plot_data]{SpliceWiz::makeMatrix()}}}
 }
 \value{
 a data matrix