Recent changes to expression_list

expression_list modified by Keith Ching

Keith Ching — Sat, 04 Mar 2017 00:59:47 -0000

--- v7
+++ v8
@@ -12,3 +12,6 @@
 Note: only categorical metadata with a limited number of unique values can be used for the color bar.

 Example [query](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&expcnv_colors=red+blue+green+violet+orange+yellow+black&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=1&cnvminbp=10000&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=expression_list&METACOLORS=green+blue&venn_segment=none&sort=mean&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&cnvamp=2&venncnvgene1=%3e1&tissues=ALL&affy_source=TCGA-BRCA-RSEM&expmut_numresults=25&vennexpgene1=%3e10&venncnvgene2=%3e1&vennexpgene4=%3e10&expcore_colors=red+blue+green+violet+orange+yellow+black&venncnvgene5=%3e1&mut_expression_method=t-test&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=braf+kras+tp53&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)
+
+
+Dev: add stacked barplot if CNV/EXP plot is checked, limit 40 genes

expression_list modified by Keith Ching

Keith Ching — Wed, 02 Mar 2016 20:09:26 -0000

--- v6
+++ v7
@@ -7,7 +7,7 @@
 *HUGO* : space separated list of genes to obtain expression for. (required)
 *EXPRESSION* : data source (required)
 *CNV/EXP plot* : plot a heatmap (optional)
-*Metadata* : add metadata color bar to heatmap (optional) (required CNV/EXP plot) The plot must be plotted once for metadata selections to appear. Then select a metadata feature and resubmit to re-render the plot with the colored metadata.
+*Metadata* : add metadata color bar to heatmap (optional) (required CNV/EXP plot) The plot must be plotted once for metadata selections to appear. Then select a metadata feature and resubmit to re-render the plot with the colored metadata. [Example with meta heatmap](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&combination_id2=NONE&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=NONE&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=1&cnvminbp=10000&compound_source=NONE&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&metadata_names=3899+PAM50.RNASEQ+&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=expression_list&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&dataset_name=NONE&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&showplot=on&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=TCGA-BRCA-RSEM&vennexpgene1=%3e10&expmut_numresults=25&vennexpgene4=%3e10&venncnvgene2=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&mut_expression_method=t-test&venncnvgene5=%3e1&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&rnai_source=NONE&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&tabledump_table=cells&mirna_source=NONE&metadata_source=TCGA-BRCA&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=esr1+erbb2+aurka+mki67+pgr&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)

 Note: only categorical metadata with a limited number of unique values can be used for the color bar.

expression_list modified by Keith Ching

Keith Ching — Wed, 25 Nov 2015 01:38:23 -0000

--- v5
+++ v6
@@ -10,3 +10,5 @@
 *Metadata* : add metadata color bar to heatmap (optional) (required CNV/EXP plot) The plot must be plotted once for metadata selections to appear. Then select a metadata feature and resubmit to re-render the plot with the colored metadata.

 Note: only categorical metadata with a limited number of unique values can be used for the color bar.  
+
+Example [query](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&expcnv_colors=red+blue+green+violet+orange+yellow+black&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=1&cnvminbp=10000&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=expression_list&METACOLORS=green+blue&venn_segment=none&sort=mean&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&cnvamp=2&venncnvgene1=%3e1&tissues=ALL&affy_source=TCGA-BRCA-RSEM&expmut_numresults=25&vennexpgene1=%3e10&venncnvgene2=%3e1&vennexpgene4=%3e10&expcore_colors=red+blue+green+violet+orange+yellow+black&venncnvgene5=%3e1&mut_expression_method=t-test&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=braf+kras+tp53&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)

expression_list modified by Keith Ching

Keith Ching — Tue, 06 Jan 2015 08:51:30 -0000

--- v4
+++ v5
@@ -7,6 +7,6 @@
 *HUGO* : space separated list of genes to obtain expression for. (required)
 *EXPRESSION* : data source (required)
 *CNV/EXP plot* : plot a heatmap (optional)
-*Metadata* : add metadata color bar to heatmap (optional) (required CNV/EXP plot) must be plotted once for metadata selections to appear. Then select a metadata feature and resubmit to re-render the plot.
+*Metadata* : add metadata color bar to heatmap (optional) (required CNV/EXP plot) The plot must be plotted once for metadata selections to appear. Then select a metadata feature and resubmit to re-render the plot with the colored metadata.

 Note: only categorical metadata with a limited number of unique values can be used for the color bar.

expression_list modified by Keith Ching

Keith Ching — Tue, 06 Jan 2015 08:49:02 -0000

--- v3
+++ v4
@@ -2,7 +2,7 @@

 [Instructions]

-expression_list is a way to obtain expression data in a table format. Two tables are output, one with the raw values as stored in the database, the other as median centered. This method is meant as a way to extract small amounts of data and create custom heatmaps. If you have > 100 genes, it would be more efficient to download the RData object. (links to RData objects are shown after doing an expression_cor search)
+expression_list is a way to obtain expression data in a table format. Two tables are output, one with the raw values as stored in the database, the other as median centered. This method is meant as a way to extract small amounts of data and create custom heatmaps. If you have > 100 genes, it would be more efficient to download the RData object. (links to RData objects are shown after doing an [expression_cor] search)

 *HUGO* : space separated list of genes to obtain expression for. (required)
 *EXPRESSION* : data source (required)

expression_list modified by Keith Ching

Keith Ching — Tue, 06 Jan 2015 08:47:49 -0000

--- v2
+++ v3
@@ -1,3 +1,5 @@
+[[img src=expression_list_table.png alt=table]]
+
 [Instructions]

 expression_list is a way to obtain expression data in a table format. Two tables are output, one with the raw values as stored in the database, the other as median centered. This method is meant as a way to extract small amounts of data and create custom heatmaps. If you have > 100 genes, it would be more efficient to download the RData object. (links to RData objects are shown after doing an expression_cor search)

expression_list modified by Keith Ching

Keith Ching — Tue, 06 Jan 2015 08:46:43 -0000

expression_list modified by Keith Ching

Keith Ching — Tue, 06 Jan 2015 08:45:04 -0000

[Instructions]

expression_list is a way to obtain expression data in a table format. Two tables are output, one with the raw values as stored in the database, the other as median centered. This method is meant as a way to extract small amounts of data and create custom heatmaps. If you have > 100 genes, it would be more efficient to download the RData object. (links to RData objects are shown after doing an expression_cor search)

HUGO : space separated list of genes to obtain expression for. (required)
EXPRESSION : data source (required)
CNV/EXP plot : plot a heatmap (optional)
Metadata : add metadata color bar to heatmap (optional) (required CNV/EXP plot) must be plotted once for metadata selections to appear. Then select a metadata feature and resubmit to re-render the plot.

Note: only categorical metadata with a limited number of unique values can be used for the color bar.