Mercurial > repos > mingchen0919 > rmarkdown_feature_counts

changeset 13:eb51eca6cdf1 draft

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update
author mingchen0919
date Fri, 29 Dec 2017 15:00:59 -0500
parents 7a2369ab4f84
children bfa6440d01a3
files rmarkdown_feature_counts.Rmd rmarkdown_feature_counts.xml
diffstat 2 files changed, 9 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/rmarkdown_feature_counts.Rmd	Fri Dec 29 14:24:54 2017 -0500
+++ b/rmarkdown_feature_counts.Rmd	Fri Dec 29 15:00:59 2017 -0500
@@ -85,8 +85,13 @@
 ```{r}
 colnames(res$counts) = strsplit(opt$input_bam_names, ',')[[1]]
 # write count into csv file
-write.csv(res$counts, file = 'feature_counts.csv', row.names = TRUE)
-datatable(res$counts)
+write.table(res$counts, file = 'feature_counts.txt')
+```
+
+Display the first 100 rows.
+
+```{r}
+datatable(head(res$counts, 100))
 ```
 
 # Save results into RData file
--- a/rmarkdown_feature_counts.xml	Fri Dec 29 14:24:54 2017 -0500
+++ b/rmarkdown_feature_counts.xml	Fri Dec 29 15:00:59 2017 -0500
@@ -177,7 +177,8 @@
               hidden="false"/>
         <data name="feature_counts" format="rdata" label="feature counts" from_work_dir="feature_counts.RData"
               hidden="false"/>
-        <data name="feature_counts_csv" format="csv" label="feature counts in csv" from_work_dir="feature_counts.csv"
+        <data name="feature_counts_csv" format="tabular" label="feature counts (.txt)"
+              from_work_dir="feature_counts.txt"
               hidden="false"/>
     </outputs>
     <help><![CDATA[some help text]]></help>