diff --git a/inst/content/custom_genes.png b/inst/content/custom_genes.png new file mode 100644 index 0000000..ef9201b Binary files /dev/null and b/inst/content/custom_genes.png differ diff --git a/inst/content/gene_selector.png b/inst/content/gene_selector.png new file mode 100644 index 0000000..d38fcf8 Binary files /dev/null and b/inst/content/gene_selector.png differ diff --git a/inst/content/gsea.png b/inst/content/gsea.png new file mode 100644 index 0000000..226455c Binary files /dev/null and b/inst/content/gsea.png differ diff --git a/inst/content/help.md b/inst/content/help.md index ae64803..bfa7ac9 100644 --- a/inst/content/help.md +++ b/inst/content/help.md @@ -16,6 +16,8 @@ from a dropdown menu. To paste your genes as a whitespace separated list of either HGNC symbols or Ensembl gene IDs (in the form `ENSG00000164362`), change the top dropdown from "Select from list" to the desired input method. +![Screenshot of the gene selector](gene_selector.png) + ## Which information does the tool give for my genes of interest? Once your genes have been selected, the user interface will automatically switch @@ -33,6 +35,8 @@ their top right corner): 4. A detailed table (downloadable as CSV) including scores, ranks and percentiles as well as the computed parameters for your genes. +![Screenshot of information on custom genes](custom_genes.png) + ## How can I change the parameters of the method? The panel on the left side offers multiple controls to change the parameters of @@ -46,6 +50,8 @@ as well as their weight contributing to that score. These are the criteria: | Expression level | The median expression level (logarithmic) is determined for each gene across all samples. Alternatively, it is possible to select the mean expression. | 25% | | Expression variation | Measure of the variation of a gene’s expression between samples. By default, the interquartile range (IQR) normalized by the median is used. Other options include the IQR itself, the standard deviation and the coefficient of variation. | -25% | +![Screenshot of the method parameter controls](method_parameters.png) + ## What does the GSEA tab do? The "GSEA" tab provides a simple gene set enrichment analysis using @@ -54,6 +60,8 @@ of over-representation of annotated genes in the top part of the ranking which is a way to insinuate the biological or at least scientific relevance of the scoring. +![Screenshot of the GSEA plot](gsea.png) + ## How can I perform analyses of ubiquity relative to my own expression dataset? Because of the computational requirements we can not publicly provide this diff --git a/inst/content/method_parameters.png b/inst/content/method_parameters.png new file mode 100644 index 0000000..42d92be Binary files /dev/null and b/inst/content/method_parameters.png differ diff --git a/inst/content/style.css b/inst/content/style.css index 3390f22..1085b71 100644 --- a/inst/content/style.css +++ b/inst/content/style.css @@ -35,4 +35,9 @@ h5 { .container th, .container td { padding: 4px; +} + +.container img { + max-width: 100%; + height: auto; } \ No newline at end of file