updated flowchart

docs/additional-analyses.html

@@ -189,8 +189,8 @@ <h2><span class="header-section-number">4.1</span> Diagnostic panels content ove
 </blockquote>
 <p>We used ten common diagnostic panels that can be ordered for kidney disease analysis and extracted the screened genes from them.
 Here we show the overlap of the genes in the different panels.</p>
-<div class="plotly html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-ad8374710103433680b4" style="width:100%;height:480px;"></div>
-<script type="application/json" data-for="htmlwidget-ad8374710103433680b4">{"x":{"data":[{"orientation":"v","width":[0.9,0.9,0.9,0.9,0.9,0.9,0.899999999999999,0.899999999999999],"base":[0,0,0,0,0,0,0,0],"x":[2,3,4,5,6,7,8,9],"y":[134,73,60,41,40,45,52,53],"text":["source_count:  2<br />n: 134<br />fill_color: Gray","source_count:  3<br />n:  73<br />fill_color: Gray","source_count:  4<br />n:  60<br />fill_color: Gray","source_count:  5<br />n:  41<br />fill_color: Gray","source_count:  6<br />n:  40<br />fill_color: Gray","source_count:  7<br />n:  45<br />fill_color: Gray","source_count:  8<br />n:  52<br />fill_color: Gray","source_count:  9<br />n:  53<br />fill_color: Gray"],"type":"bar","textposition":"none","marker":{"autocolorscale":false,"color":"rgba(190,190,190,1)","line":{"width":1.88976377952756,"color":"transparent"}},"name":"Gray","legendgroup":"Gray","showlegend":true,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null},{"orientation":"v","width":0.899999999999999,"base":0,"x":[10],"y":[56],"text":"source_count: 10<br />n:  56<br />fill_color: Green","type":"bar","textposition":"none","marker":{"autocolorscale":false,"color":"rgba(0,255,0,1)","line":{"width":1.88976377952756,"color":"transparent"}},"name":"Green","legendgroup":"Green","showlegend":true,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null},{"orientation":"v","width":0.9,"base":0,"x":[1],"y":[402],"text":"source_count:  1<br />n: 402<br />fill_color: Red","type":"bar","textposition":"none","marker":{"autocolorscale":false,"color":"rgba(255,0,0,1)","line":{"width":1.88976377952756,"color":"transparent"}},"name":"Red","legendgroup":"Red","showlegend":true,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null},{"x":[2,3,4,5,6,7,8,9],"y":[134,73,60,41,40,45,52,53],"text":["14%","7.6%","6.3%","4.3%","4.2%","4.7%","5.4%","5.5%"],"hovertext":["source_count:  2<br />n: 134<br />fill_color: Gray<br />paste0(round(percentage, 1), \"%\"): 14%","source_count:  3<br />n:  73<br />fill_color: Gray<br />paste0(round(percentage, 1), \"%\"): 7.6%","source_count:  4<br />n:  60<br />fill_color: Gray<br />paste0(round(percentage, 1), \"%\"): 6.3%","source_count:  5<br />n:  41<br />fill_color: Gray<br />paste0(round(percentage, 1), \"%\"): 4.3%","source_count:  6<br />n:  40<br />fill_color: Gray<br />paste0(round(percentage, 1), \"%\"): 4.2%","source_count:  7<br />n:  45<br />fill_color: Gray<br />paste0(round(percentage, 1), \"%\"): 4.7%","source_count:  8<br />n:  52<br />fill_color: Gray<br />paste0(round(percentage, 1), \"%\"): 5.4%","source_count:  9<br />n:  53<br />fill_color: Gray<br />paste0(round(percentage, 1), \"%\"): 5.5%"],"textfont":{"size":14.6645669291339,"color":"rgba(0,0,0,1)"},"type":"scatter","mode":"text","hoveron":"points","name":"Gray","legendgroup":"Gray","showlegend":false,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null},{"x":[10],"y":[56],"text":"5.9%","hovertext":"source_count: 10<br />n:  56<br />fill_color: Green<br />paste0(round(percentage, 1), \"%\"): 5.9%","textfont":{"size":14.6645669291339,"color":"rgba(0,0,0,1)"},"type":"scatter","mode":"text","hoveron":"points","name":"Green","legendgroup":"Green","showlegend":false,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null},{"x":[1],"y":[402],"text":"42.1%","hovertext":"source_count:  1<br />n: 402<br />fill_color: Red<br />paste0(round(percentage, 1), \"%\"): 42.1%","textfont":{"size":14.6645669291339,"color":"rgba(0,0,0,1)"},"type":"scatter","mode":"text","hoveron":"points","name":"Red","legendgroup":"Red","showlegend":false,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null}],"layout":{"margin":{"t":43.7625570776256,"r":7.30593607305936,"b":40.1826484018265,"l":43.1050228310502},"font":{"color":"rgba(0,0,0,1)","family":"","size":14.6118721461187},"title":{"text":"Number of genes in 10 clinical diagnostic panels for kidney disease (n = 956)","font":{"color":"rgba(0,0,0,1)","family":"","size":17.5342465753425},"x":0,"xref":"paper"},"xaxis":{"domain":[0,1],"automargin":true,"type":"linear","autorange":false,"range":[0.0550000000000001,10.945],"tickmode":"array","ticktext":["1","2","3","4","5","6","7","8","9","10"],"tickvals":[1,2,3,4,5,6,7,8,9,10],"categoryorder":"array","categoryarray":["1","2","3","4","5","6","7","8","9","10"],"nticks":null,"ticks":"","tickcolor":null,"ticklen":3.65296803652968,"tickwidth":0,"showticklabels":true,"tickfont":{"color":"rgba(77,77,77,1)","family":"","size":11.689497716895},"tickangle":-0,"showline":false,"linecolor":null,"linewidth":0,"showgrid":true,"gridcolor":"rgba(235,235,235,1)","gridwidth":0.66417600664176,"zeroline":false,"anchor":"y","title":{"text":"Count of panels","font":{"color":"rgba(0,0,0,1)","family":"","size":14.6118721461187}},"hoverformat":".2f"},"yaxis":{"domain":[0,1],"automargin":true,"type":"linear","autorange":false,"range":[-20.1,422.1],"tickmode":"array","ticktext":["0","100","200","300","400"],"tickvals":[0,100,200,300,400],"categoryorder":"array","categoryarray":["0","100","200","300","400"],"nticks":null,"ticks":"","tickcolor":null,"ticklen":3.65296803652968,"tickwidth":0,"showticklabels":true,"tickfont":{"color":"rgba(77,77,77,1)","family":"","size":11.689497716895},"tickangle":-0,"showline":false,"linecolor":null,"linewidth":0,"showgrid":true,"gridcolor":"rgba(235,235,235,1)","gridwidth":0.66417600664176,"zeroline":false,"anchor":"x","title":{"text":"Number of Genes","font":{"color":"rgba(0,0,0,1)","family":"","size":14.6118721461187}},"hoverformat":".2f"},"shapes":[{"type":"rect","fillcolor":null,"line":{"color":null,"width":0,"linetype":[]},"yref":"paper","xref":"paper","x0":0,"x1":1,"y0":0,"y1":1}],"showlegend":true,"legend":{"bgcolor":null,"bordercolor":null,"borderwidth":0,"font":{"color":"rgba(0,0,0,1)","family":"","size":11.689497716895},"title":{"text":"","font":{"color":"rgba(0,0,0,1)","family":"","size":14.6118721461187}}},"hovermode":"closest","barmode":"relative"},"config":{"doubleClick":"reset","modeBarButtonsToAdd":["hoverclosest","hovercompare"],"showSendToCloud":false},"source":"A","attrs":{"f6f357fb41d":{"x":{},"y":{},"fill":{},"type":"bar"},"f6f5309f75b":{"x":{},"y":{},"fill":{},"label":{}}},"cur_data":"f6f357fb41d","visdat":{"f6f357fb41d":["function (y) ","x"],"f6f5309f75b":["function (y) ","x"]},"highlight":{"on":"plotly_click","persistent":false,"dynamic":false,"selectize":false,"opacityDim":0.2,"selected":{"opacity":1},"debounce":0},"shinyEvents":["plotly_hover","plotly_click","plotly_selected","plotly_relayout","plotly_brushed","plotly_brushing","plotly_clickannotation","plotly_doubleclick","plotly_deselect","plotly_afterplot","plotly_sunburstclick"],"base_url":"https://plot.ly"},"evals":[],"jsHooks":[]}</script>
+<div class="plotly html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-b03a3c63cf6daedc651f" style="width:100%;height:480px;"></div>
+<script type="application/json" data-for="htmlwidget-b03a3c63cf6daedc651f">{"x":{"data":[{"orientation":"v","width":[0.9,0.9,0.9,0.9,0.9,0.9,0.899999999999999,0.899999999999999],"base":[0,0,0,0,0,0,0,0],"x":[2,3,4,5,6,7,8,9],"y":[134,73,60,41,40,45,52,53],"text":["source_count:  2<br />n: 134<br />fill_color: Gray","source_count:  3<br />n:  73<br />fill_color: Gray","source_count:  4<br />n:  60<br />fill_color: Gray","source_count:  5<br />n:  41<br />fill_color: Gray","source_count:  6<br />n:  40<br />fill_color: Gray","source_count:  7<br />n:  45<br />fill_color: Gray","source_count:  8<br />n:  52<br />fill_color: Gray","source_count:  9<br />n:  53<br />fill_color: Gray"],"type":"bar","textposition":"none","marker":{"autocolorscale":false,"color":"rgba(190,190,190,1)","line":{"width":1.88976377952756,"color":"transparent"}},"name":"Gray","legendgroup":"Gray","showlegend":true,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null},{"orientation":"v","width":0.899999999999999,"base":0,"x":[10],"y":[56],"text":"source_count: 10<br />n:  56<br />fill_color: Green","type":"bar","textposition":"none","marker":{"autocolorscale":false,"color":"rgba(0,255,0,1)","line":{"width":1.88976377952756,"color":"transparent"}},"name":"Green","legendgroup":"Green","showlegend":true,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null},{"orientation":"v","width":0.9,"base":0,"x":[1],"y":[402],"text":"source_count:  1<br />n: 402<br />fill_color: Red","type":"bar","textposition":"none","marker":{"autocolorscale":false,"color":"rgba(255,0,0,1)","line":{"width":1.88976377952756,"color":"transparent"}},"name":"Red","legendgroup":"Red","showlegend":true,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null},{"x":[2,3,4,5,6,7,8,9],"y":[134,73,60,41,40,45,52,53],"text":["14%","7.6%","6.3%","4.3%","4.2%","4.7%","5.4%","5.5%"],"hovertext":["source_count:  2<br />n: 134<br />fill_color: Gray<br />paste0(round(percentage, 1), \"%\"): 14%","source_count:  3<br />n:  73<br />fill_color: Gray<br />paste0(round(percentage, 1), \"%\"): 7.6%","source_count:  4<br />n:  60<br />fill_color: Gray<br />paste0(round(percentage, 1), \"%\"): 6.3%","source_count:  5<br />n:  41<br />fill_color: Gray<br />paste0(round(percentage, 1), \"%\"): 4.3%","source_count:  6<br />n:  40<br />fill_color: Gray<br />paste0(round(percentage, 1), \"%\"): 4.2%","source_count:  7<br />n:  45<br />fill_color: Gray<br />paste0(round(percentage, 1), \"%\"): 4.7%","source_count:  8<br />n:  52<br />fill_color: Gray<br />paste0(round(percentage, 1), \"%\"): 5.4%","source_count:  9<br />n:  53<br />fill_color: Gray<br />paste0(round(percentage, 1), \"%\"): 5.5%"],"textfont":{"size":14.6645669291339,"color":"rgba(0,0,0,1)"},"type":"scatter","mode":"text","hoveron":"points","name":"Gray","legendgroup":"Gray","showlegend":false,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null},{"x":[10],"y":[56],"text":"5.9%","hovertext":"source_count: 10<br />n:  56<br />fill_color: Green<br />paste0(round(percentage, 1), \"%\"): 5.9%","textfont":{"size":14.6645669291339,"color":"rgba(0,0,0,1)"},"type":"scatter","mode":"text","hoveron":"points","name":"Green","legendgroup":"Green","showlegend":false,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null},{"x":[1],"y":[402],"text":"42.1%","hovertext":"source_count:  1<br />n: 402<br />fill_color: Red<br />paste0(round(percentage, 1), \"%\"): 42.1%","textfont":{"size":14.6645669291339,"color":"rgba(0,0,0,1)"},"type":"scatter","mode":"text","hoveron":"points","name":"Red","legendgroup":"Red","showlegend":false,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null}],"layout":{"margin":{"t":43.7625570776256,"r":7.30593607305936,"b":40.1826484018265,"l":43.1050228310502},"font":{"color":"rgba(0,0,0,1)","family":"","size":14.6118721461187},"title":{"text":"Number of genes in 10 clinical diagnostic panels for kidney disease (n = 956)","font":{"color":"rgba(0,0,0,1)","family":"","size":17.5342465753425},"x":0,"xref":"paper"},"xaxis":{"domain":[0,1],"automargin":true,"type":"linear","autorange":false,"range":[0.0550000000000001,10.945],"tickmode":"array","ticktext":["1","2","3","4","5","6","7","8","9","10"],"tickvals":[1,2,3,4,5,6,7,8,9,10],"categoryorder":"array","categoryarray":["1","2","3","4","5","6","7","8","9","10"],"nticks":null,"ticks":"","tickcolor":null,"ticklen":3.65296803652968,"tickwidth":0,"showticklabels":true,"tickfont":{"color":"rgba(77,77,77,1)","family":"","size":11.689497716895},"tickangle":-0,"showline":false,"linecolor":null,"linewidth":0,"showgrid":true,"gridcolor":"rgba(235,235,235,1)","gridwidth":0.66417600664176,"zeroline":false,"anchor":"y","title":{"text":"Count of panels","font":{"color":"rgba(0,0,0,1)","family":"","size":14.6118721461187}},"hoverformat":".2f"},"yaxis":{"domain":[0,1],"automargin":true,"type":"linear","autorange":false,"range":[-20.1,422.1],"tickmode":"array","ticktext":["0","100","200","300","400"],"tickvals":[0,100,200,300,400],"categoryorder":"array","categoryarray":["0","100","200","300","400"],"nticks":null,"ticks":"","tickcolor":null,"ticklen":3.65296803652968,"tickwidth":0,"showticklabels":true,"tickfont":{"color":"rgba(77,77,77,1)","family":"","size":11.689497716895},"tickangle":-0,"showline":false,"linecolor":null,"linewidth":0,"showgrid":true,"gridcolor":"rgba(235,235,235,1)","gridwidth":0.66417600664176,"zeroline":false,"anchor":"x","title":{"text":"Number of Genes","font":{"color":"rgba(0,0,0,1)","family":"","size":14.6118721461187}},"hoverformat":".2f"},"shapes":[{"type":"rect","fillcolor":null,"line":{"color":null,"width":0,"linetype":[]},"yref":"paper","xref":"paper","x0":0,"x1":1,"y0":0,"y1":1}],"showlegend":true,"legend":{"bgcolor":null,"bordercolor":null,"borderwidth":0,"font":{"color":"rgba(0,0,0,1)","family":"","size":11.689497716895},"title":{"text":"","font":{"color":"rgba(0,0,0,1)","family":"","size":14.6118721461187}}},"hovermode":"closest","barmode":"relative"},"config":{"doubleClick":"reset","modeBarButtonsToAdd":["hoverclosest","hovercompare"],"showSendToCloud":false},"source":"A","attrs":{"1432406220b3":{"x":{},"y":{},"fill":{},"type":"bar"},"14326a50e8ca":{"x":{},"y":{},"fill":{},"label":{}}},"cur_data":"1432406220b3","visdat":{"1432406220b3":["function (y) ","x"],"14326a50e8ca":["function (y) ","x"]},"highlight":{"on":"plotly_click","persistent":false,"dynamic":false,"selectize":false,"opacityDim":0.2,"selected":{"opacity":1},"debounce":0},"shinyEvents":["plotly_hover","plotly_click","plotly_selected","plotly_relayout","plotly_brushed","plotly_brushing","plotly_clickannotation","plotly_doubleclick","plotly_deselect","plotly_afterplot","plotly_sunburstclick"],"base_url":"https://plot.ly"},"evals":[],"jsHooks":[]}</script>
 
 </div>
 </div>