From 66c2c7c7b91623bed1f31c0b5ed7d2eabf1bae35 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Maciek=20B=C4=85k?= Date: Wed, 10 Jan 2024 16:22:05 +0100 Subject: [PATCH] refactor: update the HTML report (#30) --- resources/activities-3ss.html | 99 +++++++++++++++ resources/activities-5ss.html | 99 +++++++++++++++ resources/activities-pas.html | 99 +++++++++++++++ resources/exon-inclusion.html | 113 +++++++++++++++++ resources/gene-expression.html | 106 ++++++++++++++++ resources/mapp_logo.png | Bin 0 -> 31244 bytes resources/pas-expression.html | 178 +++++++++++++++++++++++++++ resources/template.html | 57 +++++---- resources/transcript-expression.html | 105 ++++++++++++++++ scripts/generate-final-report.py | 91 +++++++++----- 10 files changed, 896 insertions(+), 51 deletions(-) create mode 100644 resources/activities-3ss.html create mode 100644 resources/activities-5ss.html create mode 100644 resources/activities-pas.html create mode 100644 resources/exon-inclusion.html create mode 100644 resources/gene-expression.html create mode 100644 resources/mapp_logo.png create mode 100644 resources/pas-expression.html create mode 100644 resources/transcript-expression.html diff --git a/resources/activities-3ss.html b/resources/activities-3ss.html new file mode 100644 index 00000000..8798ab3d --- /dev/null +++ b/resources/activities-3ss.html @@ -0,0 +1,99 @@ + + + + MAPP reports + + +
+
+ +

MAPP Report

+

Test run with reduced parameters on a sampled dataset

+
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+ This is a summary report for a MAPP run. + Motif count matrices are located under: ../modules/CREATE_SITECOUNT_MATRICES/output, + unless external pre-computer resources were specified for this specific workflow execution. + In such case please refer to the pipeline's configuration file and inspect the paths provided + under the field: MAE_sitecount_matrices. +
+
+ Fitted motif activities as well as calculated activity z-scores and their statistical significance + are stored in a tab-separated formatted (TSV) table. + Rows of this table denote various sequence motifs in specific sliding windows whereas subsequent columns follow the + structure below: +
+
+ ID : unique ID of a sequence motif in a specific sliding window +
+ activities_{sampleID} : motif activities in distinct RNA-Seq samples +
+ deltas_{sampleID} : standard deviations of motif activities +
+ zscores_{sampleID} : z-scores of motif activities +
+ combined.Zscore : overall z-score for a given motif, combined over all samples +
+ regions_present_fraction : fraction of sites for which the motif was present in a specific window +
+ region : sliding window ID +
+ motif : short sequence motif +
+ standard_zscores_{sampleID} : standardised z-scores of motif activities +
+ pval_{sampleID} : standardised p-values of motif activities +
+ corr_pval_{sampleID} : p-values corrected for multiple hypothesis testing +
+ combined.standard.Zscore : combined standardised z-scores +
+ max.abs.standard.Zscore : maximum absolute standardised z-score +
+ significance-marker : statistical significance marker for this motif in this sliding window +
+
+
+
+ + + +  + + + +
+ + diff --git a/resources/activities-5ss.html b/resources/activities-5ss.html new file mode 100644 index 00000000..a15348d1 --- /dev/null +++ b/resources/activities-5ss.html @@ -0,0 +1,99 @@ + + + + MAPP reports + + +
+
+ +

MAPP Report

+

Test run with reduced parameters on a sampled dataset

+
+ + + +   + + + +   + + + +   + + + +
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+ This is a summary report for a MAPP run. + Motif count matrices are located under: ../modules/CREATE_SITECOUNT_MATRICES/output, + unless external pre-computer resources were specified for this specific workflow execution. + In such case please refer to the pipeline's configuration file and inspect the paths provided + under the field: MAE_sitecount_matrices. +
+
+ Fitted motif activities as well as calculated activity z-scores and their statistical significance + are stored in a tab-separated formatted (TSV) table. + Rows of this table denote various sequence motifs in specific sliding windows whereas subsequent columns follow the + structure below: +
+
+ ID : unique ID of a sequence motif in a specific sliding window +
+ activities_{sampleID} : motif activities in distinct RNA-Seq samples +
+ deltas_{sampleID} : standard deviations of motif activities +
+ zscores_{sampleID} : z-scores of motif activities +
+ combined.Zscore : overall z-score for a given motif, combined over all samples +
+ regions_present_fraction : fraction of sites for which the motif was present in a specific window +
+ region : sliding window ID +
+ motif : short sequence motif +
+ standard_zscores_{sampleID} : standardised z-scores of motif activities +
+ pval_{sampleID} : standardised p-values of motif activities +
+ corr_pval_{sampleID} : p-values corrected for multiple hypothesis testing +
+ combined.standard.Zscore : combined standardised z-scores +
+ max.abs.standard.Zscore : maximum absolute standardised z-score +
+ significance-marker : statistical significance marker for this motif in this sliding window +
+
+
+
+ + + +  + + + +
+ + diff --git a/resources/activities-pas.html b/resources/activities-pas.html new file mode 100644 index 00000000..c853cddd --- /dev/null +++ b/resources/activities-pas.html @@ -0,0 +1,99 @@ + + + + MAPP reports + + +
+
+ +

MAPP Report

+

Test run with reduced parameters on a sampled dataset

+
+ + + +   + + + +   + + + +   + + + +
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+ This is a summary report for a MAPP run. + Motif count matrices are located under: ../modules/KAPAC/output, + unless external pre-computer resources were specified for this specific workflow execution. + In such case please refer to the pipeline's configuration file and inspect the paths provided + under the field: KPC_sitecount_matrices. +
+
+ Fitted motif activities as well as calculated activity z-scores and their statistical significance + are stored in a tab-separated formatted (TSV) table. + Rows of this table denote various sequence motifs in specific sliding windows whereas subsequent columns follow the + structure below: +
+
+ ID : unique ID of a sequence motif in a specific sliding window +
+ activities_{sampleID} : motif activities in distinct RNA-Seq samples +
+ deltas_{sampleID} : standard deviations of motif activities +
+ zscores_{sampleID} : z-scores of motif activities +
+ combined.Zscore : overall z-score for a given motif, combined over all samples +
+ regions_present_fraction : fraction of sites for which the motif was present in a specific window +
+ region : sliding window ID +
+ motif : short sequence motif +
+ standard_zscores_{sampleID} : standardised z-scores of motif activities +
+ pval_{sampleID} : standardised p-values of motif activities +
+ corr_pval_{sampleID} : p-values corrected for multiple hypothesis testing +
+ combined.standard.Zscore : combined standardised z-scores +
+ max.abs.standard.Zscore : maximum absolute standardised z-score +
+ significance-marker : statistical significance marker for this motif in this sliding window +
+
+
+
+ + + +  + + + +
+ + diff --git a/resources/exon-inclusion.html b/resources/exon-inclusion.html new file mode 100644 index 00000000..ca7f1d82 --- /dev/null +++ b/resources/exon-inclusion.html @@ -0,0 +1,113 @@ + + + + MAPP reports + + +
+
+ +

MAPP Report

+

Test run with reduced parameters on a sampled dataset

+
+ + + +   + + + +   + + + +   + + + +
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+ Cassette exon inclusion is represented as a ratio of expression + for transcripts which include a specific exon + to all those transcripts which could have possibly included it. + Numerators and denominators of these ratios are stored separately in a tab-separated format (TSV) table. + Each row in the expression table represents a single cassette exon. The first column + specifies exon coordinates in a BED format. + Each of the next columns stores aggregated TPM values for + specific RNA-Seq samples. Columns with numerators of the inclusion fraction ratios are + denoted with an "_included" suffix whereas denominators are marked with "_total". + Please see the scheme below: +
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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Sample1_includedSample2_includedSample1_totalSample2_total...
Exon1
Exon2
Exon3
...
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+ + diff --git a/resources/gene-expression.html b/resources/gene-expression.html new file mode 100644 index 00000000..54279e55 --- /dev/null +++ b/resources/gene-expression.html @@ -0,0 +1,106 @@ + + + + MAPP reports + + +
+
+ +

MAPP Report

+

Test run with reduced parameters on a sampled dataset

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+ Gene expression has been quantified with the Salmon tool + (Patro R. et al.). +
+
+ Expression scores are stored as Transcripts-per-Milion (TPM) values in a tab-separated format (TSV) table. + Transcript expression was aggregated over all transcripts for a specific gene. + Please be aware that the TPM scores should not be used to directly compare gene expression across + distinct RNA-Seq samples. +
+
+ Each row in the expression table represents a single, unique gene. The first column + corresponds to a gene ID. Each of the next columns stores TPM values of + a specific RNA-Seq sample, as in the scheme below: +
+
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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Sample1Sample2...
Gene1
Gene2
Gene3
...
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ze1grXKiC1XbnoR6uLop>-;otyRO7LCAB^ZXR#a#9N%3k z5{!4-yRY>ayB?+5ErbWKXdbcZQFUZ*t)TqKCQhKlSkg0~jvBjibj(NYs-5S3$xh9o z77Hvc%wnXCI&9Z|o~8fSN*LiSqDO80qArJN)b#&;DPeSQb@1kbKXm4&DvPoxN3depFUu|LJUh>jzBVD%;X_Rt zU`eo`e`|7agjP>$bK~!kLoLTIKi2>H@4No*qyK99Ph`|a5VmL!Xn!gfULRcbwV=ML Oj5}>^@I=og_WuAzw{zwI literal 0 HcmV?d00001 diff --git a/resources/pas-expression.html b/resources/pas-expression.html new file mode 100644 index 00000000..ea8837ea --- /dev/null +++ b/resources/pas-expression.html @@ -0,0 +1,178 @@ + + + + MAPP reports + + +
+ +
+
+
+
+ Tandem Poly(A) sites' expression has been quantified with the PAQR tool + (Gruber A.J. et al.). +
+
+ Expression scores are stored as Transcripts-per-Milion (TPM) values in a tab-separated format (TSV) table. + Please be aware that the TPM scores should not be used to directly compare Poly(A) sites expression across + distinct RNA-Seq samples. +
+
+ Each row in the expression table represents a single, unique Poly(A) site. + The first 10 columns contain the following information: +
+ chrom : chromosome ID +
+ start : start coordinate (BED format) +
+ end : end coordinate (BED format) +
+ pas : Poly(A)-sites' ID (as in the PAS Atlas) +
+ score : minimal support level for a given Poly(A) site +
+ strand : sequence strand +
+ polyAsite_exon_idx : Poly(A) site's index on a specific terminal exon +
+ nr_polyAsites_on_exon : total number of Poly(A) sites on a specific terminal exon +
+ exon : unique terminal exon ID +
+ gene : transcript ID of this specific terminal exon +
+
+ Each of the next columns stores TPM values of + a specific RNA-Seq sample, as in the scheme below: +
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
chromstartendpasscorestrandpolyAsite_exon_idxnr_polyAsites_on_exonexongeneSample1Sample2...
PAS1
PAS2
PAS3
...
+
+
+
+ + + +  + + + +
+ + diff --git a/resources/template.html b/resources/template.html index 6b8157d8..936e6a77 100644 --- a/resources/template.html +++ b/resources/template.html @@ -1,28 +1,43 @@ - MAPP report + MAPP - - -

MAPP report

+ +
+
+ +

MAPP Report

{{AnalysisTitle}}


- -{{MainTable}} - + + + +  + + + +  + + + +  + + + +
+
+ + + +  + + + +  + + + +
+

-
-

For more information feel free to inspect the results directory manually.

-

Apart from the heatmaps it contains:

-
    -
  • BED-formatted coordinates of 3'ss, 5'ss & pas
    • -
  • TSV table with exon inclusion fractions
    • -
  • TSV tables with pas expression and relative positions
    • -
  • TSV tables with genes and transcripts quantifications
    • -
  • TSV tables with motif activities around 3'ss, 5'ss & pas
    • -
  • TXT lists of selected top motifs acting around 3'ss, 5'ss & pas
    • -
- - - diff --git a/resources/transcript-expression.html b/resources/transcript-expression.html new file mode 100644 index 00000000..4be2fb17 --- /dev/null +++ b/resources/transcript-expression.html @@ -0,0 +1,105 @@ + + + + MAPP reports + + +
+
+ +

MAPP Report

+

Test run with reduced parameters on a sampled dataset

+
+ + + +   + + + +   + + + +   + + + +
+
+ + + +   + + + +   + + + +
+
+
+
+
+ Transcript expression has been quantified with the Salmon tool + (Patro R. et al.). +
+
+ Expression scores are stored as Transcripts-per-Milion (TPM) values in a tab-separated format (TSV) table. + Please be aware that the TPM scores should not be used to directly compare transcript expression across + distinct RNA-Seq samples. +
+
+ Each row in the expression table represents a single, unique transcript. The first column + corresponds to a transcript ID. Each of the next columns stores TPM values of + a specific RNA-Seq sample, as in the scheme below: +
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Sample1Sample2...
Transcript1
Transcript2
Transcript3
...
+
+
+
+ + + +  + + + +
+ + diff --git a/scripts/generate-final-report.py b/scripts/generate-final-report.py index 020310aa..b1f8ad6a 100644 --- a/scripts/generate-final-report.py +++ b/scripts/generate-final-report.py @@ -74,41 +74,35 @@ def main(): os.path.join(options.summary_directory, "main-table.tsv"), sep="\t" ) summary = summary.round(3).fillna("NA") - print(summary) - - # set distinct columns width parameters for the table - # depending on if we run on kmers or pwms - if configfile["CSM_matrix_type"] == "kmers": - text_col_width = "10" - heatmap_col_width = "50" - heatmap_img_scaling = "30" - else: - assert configfile["CSM_matrix_type"] == "pwms" - text_col_width = "10" - heatmap_col_width = "40" - seqlogo_col_width = "10" - heatmap_img_scaling = "30" - seqlogo_img_scaling = "50" # render the HTML report template MANUALLY (for now) rendered_html = [] - for _ in range(11): + for _ in range(43): rendered_html.append(template_html[_]) - rendered_html[8] = "

" + configfile["MAPP_analysis_name"] + "

" - rendered_html.append("") + rendered_html[10] = "

" + configfile["MAPP_analysis_name"] + "

" + rendered_html.append("
") + rendered_html.append('
') rendered_html.append(" ") - if configfile["CSM_matrix_type"] == "pwms": - rendered_html.append(' ') - rendered_html.append(' ') - rendered_html.append(' ') - rendered_html.append(' ') - rendered_html.append(' ') - rendered_html.append(' ') - rendered_html.append(' ') + if configfile["CSM_matrix_type"] == "kmers": + rendered_html.append(' ') + rendered_html.append(' ') + rendered_html.append(' ') + rendered_html.append(' ') + rendered_html.append(' ') + rendered_html.append(' ') + else: + configfile["CSM_matrix_type"] == "pwms" + rendered_html.append(' ') + rendered_html.append(' ') + rendered_html.append(' ') + rendered_html.append(' ') + rendered_html.append(' ') + rendered_html.append(' ') + rendered_html.append(' ') rendered_html.append(" ") rendered_html.append(" ") for h in summary.columns.values: - rendered_html.append(" ") + rendered_html.append(' ') rendered_html.append(" ") for i, row in summary.iterrows(): rendered_html.append(" ") @@ -143,13 +137,15 @@ def main(): + ">' ) rendered_html.append(" ") rendered_html.append("
" + h + "' + h + '
") - for _ in range(12, len(template_html)): - rendered_html.append(template_html[_]) + rendered_html.append("") + rendered_html.append("
") + rendered_html.append("") + rendered_html.append("") with open(os.path.join(options.summary_directory, "report.html"), "w") as report: for line in rendered_html: @@ -161,6 +157,41 @@ def main(): os.path.join(options.summary_directory, "font-awesome-4.7.0"), ) + # copy the project logo + shutil.copy( + os.path.join(options.resources_directory, "mapp_logo.png"), + os.path.join(options.summary_directory, "mapp_logo.png"), + ) + + # copy the subsites + shutil.copy( + os.path.join(options.resources_directory, "gene-expression.html"), + os.path.join(options.summary_directory, "gene-expression.html"), + ) + shutil.copy( + os.path.join(options.resources_directory, "transcript-expression.html"), + os.path.join(options.summary_directory, "transcript-expression.html"), + ) + shutil.copy( + os.path.join(options.resources_directory, "exon-inclusion.html"), + os.path.join(options.summary_directory, "exon-inclusion.html"), + ) + shutil.copy( + os.path.join(options.resources_directory, "pas-expression.html"), + os.path.join(options.summary_directory, "pas-expression.html"), + ) + shutil.copy( + os.path.join(options.resources_directory, "activities-3ss.html"), + os.path.join(options.summary_directory, "activities-3ss.html"), + ) + shutil.copy( + os.path.join(options.resources_directory, "activities-5ss.html"), + os.path.join(options.summary_directory, "activities-5ss.html"), + ) + shutil.copy( + os.path.join(options.resources_directory, "activities-pas.html"), + os.path.join(options.summary_directory, "activities-pas.html"), + ) ##############################################################################
+ +

MAPP Report

+

Test run with reduced parameters on a sampled dataset

+
+ + + +   + + + +   + + + +   + + + +
+
+ + + +   + + + +   + + + +