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<form action="/en" method="get">
  <div class="input-group col-md-3 search_chart" style="margin-top:15px;margin-left:100px;positon:relative;" align="right">
    <input type="text" class="form-control autocompleter-node" id="keywords" name="keywords" placeholder="input keyword to search" value="" autocomplete="off">
    <div class="autocompleter " id="autocompleter-1">
      <ul class="autocompleter-list"></ul>
    </div>
    <span class="input-group-btn">
      <button type="submit" class="btn btn-info btn-search" style="margin-left:10px">Search</button>
    </span>
  </div>
</form>

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<form action="" method="post" target="_blank">
  <input type="hidden" name="csrfmiddlewaretoken" value="Bp9xgSNFcPVmxbT6ttiw5JHswaXGUEgQuXhaZ18Ql0nj2EshCKYeWB8YxWoSA3fr">
  <div class="div-class">
    <b>Read before use</b><br> 1, check data with <a href="/static/download/weishengxin_input_precheck_en.exe" target="_blank">precheck (windows version) tools</a><br> 2, data from excel, copy and paste data into the input frame<br> 3, data from txt,
    must tab-seperated, copy and paste data into the input frame<br> 4, specieal and non-English characters such as #, &lt;, &gt;, %, (, ), α are not friendly<br>
    <font color="red">5, use point as decimal separator, not comma. e.g. 3.14, not 3,14 as pi</font><br>
  </div>
  <div class="div-class">
    <b>Required</b><br>
    <!-- input box -->
    <textarea name="basic_gopathway_enrichment_bubbleplot_data" style="width:100%" rows="8" required="" placeholder="input 4 columns: term, ratio, pvalue, count
input 5 columns: term, ratio, pvalue, count, class" cols="40" id="id_basic_gopathway_enrichment_bubbleplot_data"></textarea><br>
    <!-- demo1 -->
    <button type="button" id="demo1Btn" style="font-size: 12px; background:#007DBC; color: #FFFFFF;" class="btn btn-primary">demo1</button>
    <!-- demo2 -->
    <button type="button" id="demo2Btn" style="font-size: 12px; background:#007DBC; color: #FFFFFF; margin-left: 10px;" class="btn btn-primary">demo2</button>
    <script>
      var textarea = document.getElementsByName('basic_gopathway_enrichment_bubbleplot_data')[0];
      var demo1Btn = document.getElementById('demo1Btn');
      var demo2Btn = document.getElementById('demo2Btn');
      // 定义示例1数据
      var demoData1 = `term	enrichment	pvalue	count
RNA transport	4.807258641	1.56E-05	15
Epstein-Barr virus infection	4.569261748	2.70E-05	16
HTLV-I infection	3.814616521	0.000153244	17
Tuberculosis	3.454180941	0.000351414	13
MAPK signaling pathway	3.378131581	0.000418667	16
Neurotrophin signaling pathway	3.212102971	0.000613617	10
Long-term potentiation	3.000035266	0.000999919	7
Dopaminergic synapse	2.967026455	0.001078881	10
Endocytosis	2.841316731	0.001441064	15
Herpes simplex infection	2.775219173	0.001677957	12`;
      // 定义示例2数据
      var demoData2 = `term	enrichment	pvalue	count	class
RNA transport	4.807258641	1.56E-05	15	BP
Epstein-Barr virus infection	4.569261748	2.70E-05	16	BP
HTLV-I infection	3.814616521	0.000153244	17	BP
Tuberculosis	3.454180941	0.000351414	13	CC
MAPK signaling pathway	3.378131581	0.000418667	16	CC
Neurotrophin signaling pathway	3.212102971	0.000613617	10	CC
Long-term potentiation	3.000035266	0.000999919	7	CC
Dopaminergic synapse	2.967026455	0.001078881	10	MF
Endocytosis	2.841316731	0.001441064	15	MF
Herpes simplex infection	2.775219173	0.001677957	12	MF`;
      // 事件监听器：点击示例1按钮时载入示例1数据到textarea
      demo1Btn.addEventListener('click', function() {
        if (demo1Btn.textContent === 'demo1') {
          textarea.value = demoData1;
          demo1Btn.textContent = 'reset1'; // 切换按钮文本
          demo1Btn.style.backgroundColor = '#007DBC'; // 可选：改变按钮颜色
        } else {
          textarea.value = '';
          demo1Btn.textContent = 'demo1'; // 切换回按钮文本
          demo1Btn.style.backgroundColor = '#007DBC'; // 可选：恢复按钮颜色
        }
      });
      // 事件监听器：点击示例2按钮时载入示例2数据到textarea
      demo2Btn.addEventListener('click', function() {
        if (demo2Btn.textContent === 'demo2') {
          textarea.value = demoData2;
          demo2Btn.textContent = 'reset2'; // 切换按钮文本
          demo2Btn.style.backgroundColor = '#007DBC'; // 可选：改变按钮颜色
        } else {
          textarea.value = '';
          demo2Btn.textContent = 'demo2'; // 切换回按钮文本
          demo2Btn.style.backgroundColor = '#007DBC'; // 可选：恢复按钮颜色
        }
      });
    </script>
    <!-- input checking -->
    <input type="submit" name="action" value="input_checking" id="tijiao" style="font-size: 12px; background:#90C590; margin-left: 10px;" class="btn btn-primary">
  </div>
  <div class="div-class">
    <b>Optional</b><br>
    <b>Figure size</b><br> figure width: <input type="number" name="width_size" value="6.0" max="30" style="width: 50px;" required="" step="any" id="id_width_size"><br> figure height:<input type="number" name="height_size" value="6.0" max="30"
      style="width: 50px;" required="" step="any" id="id_height_size"><br>
    <br>
    <b>Fontsize</b><br> title fontsize: <input type="number" name="title_size" value="20.0" style="width: 50px;" required="" step="any" id="id_title_size"><br> legend title fontsize: <input type="number" name="legend_title_size" value="12.0"
      style="width: 50px;" required="" step="any" id="id_legend_title_size"><br> legend text fontsize: <input type="number" name="legend_text_size" value="10.0" style="width: 50px;" required="" step="any" id="id_legend_text_size"><br> ticks fontsize:
    <input type="number" name="ticks_size" value="10.0" style="width: 50px;" required="" step="any" id="id_ticks_size"><br> axis label fontsize: <input type="number" name="label_size" value="14.0" style="width: 50px;" required="" step="any"
      id="id_label_size"><br>
    <br>
    <b>Names/Labels</b><br> title name: <textarea name="basic_gopathway_enrichment_bubbleplot_title" rows="1" cols="20" id="id_basic_gopathway_enrichment_bubbleplot_title"></textarea><br> X axis label： <textarea
      name="basic_gopathway_enrichment_bubbleplot_Xlabel" rows="1" cols="20" id="id_basic_gopathway_enrichment_bubbleplot_Xlabel"></textarea><br> Y axis label: <textarea name="basic_gopathway_enrichment_bubbleplot_Ylabel" rows="1" cols="20"
      id="id_basic_gopathway_enrichment_bubbleplot_Ylabel"></textarea><br> point size label: <textarea name="basic_gopathway_enrichment_bubbleplot_size_label" id="id_basic_gopathway_enrichment_bubbleplot_size_label" rows="1" cols="20"
      required="">count</textarea><br> colorbar title: <textarea name="basic_gopathway_enrichment_bubbleplot_color_label1" id="id_basic_gopathway_enrichment_bubbleplot_color_label1" rows="1" cols="20" required="">pvalue</textarea><br> note: if choose
    -log10 transform in colors options, labled as -log10(pvalue)<br> if choose pvlaue in colors options, labbled as pvalue<br>
    <br>
    <b>Colors (take pvalue as an example, can also be FDR, qvalue, ...)</b><br>
    <label><input type="radio" name="trans" value="-log10p" checked="true"><span>-log10 transform of pvalue</span></label><br> smaller -log10(pvalue) / larger pvalue color: <input type="text" name="basic_gopathway_enrichment_bubbleplot_lower_color1"
      value="#00FF00" id="id_basic_gopathway_enrichment_bubbleplot_lower_color1" size="4" class="colorfield_field jscolor " autocomplete="off" style="background-image: none; background-color: rgb(0, 255, 0); color: rgb(0, 0, 0);">
    <br> larger -log10(pvalue) / smaller pvalue color: <input type="text" name="basic_gopathway_enrichment_bubbleplot_upper_color1" value="#FF0000" id="id_basic_gopathway_enrichment_bubbleplot_upper_color1" size="4" class="colorfield_field jscolor "
      autocomplete="off" style="background-image: none; background-color: rgb(255, 0, 0); color: rgb(255, 255, 255);">
    <br>
    <br>
    <label><input type="radio" name="trans" value="p"><span>pvalue</span></label><br> smaller pvalue color: <input type="text" name="basic_gopathway_enrichment_bubbleplot_lower_color2" value="#FF0000"
      id="id_basic_gopathway_enrichment_bubbleplot_lower_color2" size="4" class="colorfield_field jscolor " autocomplete="off" style="background-image: none; background-color: rgb(255, 0, 0); color: rgb(255, 255, 255);">
    <br> larger pvalue color: <input type="text" name="basic_gopathway_enrichment_bubbleplot_upper_color2" value="#00FF00" id="id_basic_gopathway_enrichment_bubbleplot_upper_color2" size="4" class="colorfield_field jscolor " autocomplete="off"
      style="background-image: none; background-color: rgb(0, 255, 0); color: rgb(0, 0, 0);">
    <br>
    <br>
    <b>Point size</b><br> samall point size: <input type="number" name="point_small" value="2.0" style="width: 50px;" required="" step="any" id="id_point_small"><br> big point size： <input type="number" name="point_big" value="6.0"
      style="width: 50px;" required="" step="any" id="id_point_big"><br>
    <br>
    <b>Order</b><br>
    <label><input type="radio" name="order" value="2+" checked="true"><span>column 2, big -&gt; small</span></label>
    <label><input type="radio" name="order" value="2-"><span>column 2, small -&gt; big</span></label><br>
    <label><input type="radio" name="order" value="3+"><span>column 3, big -&gt; small</span></label>
    <label><input type="radio" name="order" value="3-"><span>column 3, small -&gt; big</span></label><br>
    <label><input type="radio" name="order" value="4+"><span>column 4, big -&gt; small</span></label>
    <label><input type="radio" name="order" value="4-"><span>column 4, small -&gt; big</span></label><br>
    <label><input type="radio" name="order" value="0"><span>original order</span></label><br>
    <br>
    <b>Font family</b><br>
    <label><input type="radio" name="fontfamily" value="Times"><span>Times New Roman</span></label>
    <label><input type="radio" name="fontfamily" value="ArialMT" checked="true"><span>Arial</span></label><br>
    <br>
    <input type="submit" value="Submit" id="tijiao" class="btn btn-primary">
  </div>
</form>

Text Content

Search
test account: test Password: bio123456
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ALL modules
Basic plot pie plot
bar plot
line plot
scatter plot
Genome SNP density
Chrom distibution
Peak venn
Circos plot
Transcriptome Heatmap
Volcano Plot
Violin Plot
Bubble plot
Chord plot
Epigenome Metagene plot
Motif plot
Clinical plot forest plot
KM plot
ROC curve
Miscellaneous Map
PCA

Read before use
1, check data with precheck (windows version) tools
2, data from excel, copy and paste data into the input frame
3, data from txt, must tab-seperated, copy and paste data into the input frame
4, specieal and non-English characters such as #, <, >, %, (, ), α are not
friendly
5, use point as decimal separator, not comma. e.g. 3.14, not 3,14 as pi

Required

demo1 demo2
Optional
Figure size
figure width:
figure height:

Fontsize
title fontsize:
legend title fontsize:
legend text fontsize:
ticks fontsize:
axis label fontsize:

Names/Labels
title name:
X axis label：
Y axis label:
point size label: count
colorbar title: pvalue
note: if choose -log10 transform in colors options, labled as -log10(pvalue)
if choose pvlaue in colors options, labbled as pvalue

Colors (take pvalue as an example, can also be FDR, qvalue, ...)
-log10 transform of pvalue
smaller -log10(pvalue) / larger pvalue color:
larger -log10(pvalue) / smaller pvalue color:

pvalue
smaller pvalue color:
larger pvalue color:

Point size
samall point size:
big point size：

Order
column 2, big -> small column 2, small -> big
column 3, big -> small column 3, small -> big
column 4, big -> small column 4, small -> big
original order

Font family
Times New Roman Arial




GO, PATHWAY ENRICHMENT BUBBLE PLOT

Introduction
Bubble plot is generally used in GO, KEGG pathway enrichment analysis, in which
p values are represented by colors, gene counts are represented by bubble size.
Please use GO, Pathway Enrichment Analysis or metascape to get the enrichment
results, and then plot. Reference: ggplot2 R package
Input data instructions
Input data contain 4 columns: the first column is GO or KEGG Pathway term
(display in Y axis); the second column is enrichment (display in X, if no,
replace by others, such as gene ratio, -log10(p), count; the third column is p
(or FDR), represents colors; the fourth colunn is gene count (size of bubble).
Optional for fifth columns, plot by class with facet, for example BP, CC, MF.
Paper example
Honghua extract mediated potent inhibition of COVID-19 host cell pathways
Writing tips
Dot plot of the KEGG pathway enrichment analysis. The horizontal axis represents
the gene ratio, while the vertical axis represents the enriched pathway name.
The color scale indicates different thresholds of the p-value, and the size of
the dot indicates the number of genes corresponding to each pathway.


Input Example Output

1) How to plot?
1, Put data in excel according to the example format.
2, Copy and paste into input frame.
3, Input pre-checking button to check input
4, After checking pass, select parameters, submit and download

2) How to cite?
3000+ papers in (Google Scholar)
Tang D, Chen M, Huang X, Zhang G, Zeng L, Zhang G, Wu S, Wang Y. SRplot: A free
online platform for data visualization and graphing. PLoS One. 2023 Nov
9;18(11):e0294236. doi: 10.1371/journal.pone.0294236. PMID: 37943830.

3) FAQs



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