Mercurial > repos > greg > kaks_analysis_distribution

changeset 0:6e0f0227283b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Fri, 17 Mar 2017 07:47:15 -0400
parents
children d6f8c3d739b9
files .shed.yml kaks_analysis_distribution.R kaks_analysis_distribution.xml test-data/components.tabular test-data/kaks.tabular test-data/output.pdf
diffstat 6 files changed, 345 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Fri Mar 17 07:47:15 2017 -0400
@@ -0,0 +1,11 @@
+name: plant_tribes_kaks_analysis_barplot
+owner: iuc
+description: |
+  Contains a tool that draws a barplot of the significant components in the ks distribution.
+homepage_url: https://github.com/dePamphilis/PlantTribes
+long_description: |
+  Contains a tool that draws a barplot of the significant components in the ks distribution.
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/plant_tribes/visualization
+type: unrestricted
+categories:
+- Phylogenetics
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kaks_analysis_distribution.R	Fri Mar 17 07:47:15 2017 -0400
@@ -0,0 +1,115 @@
+#!/usr/bin/env Rscript
+
+suppressPackageStartupMessages(library("optparse"))
+
+option_list <- list(
+    make_option(c("-c", "--components_input"), action="store", dest="components_input", help="Ks significant components input dataset"),
+    make_option(c("-k", "--kaks_input"), action="store", dest="kaks_input", help="KaKs analysis input dataset"),
+    make_option(c("-o", "--output"), action="store", dest="output", help="Output dataset")
+)
+
+parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
+args <- parse_args(parser, positional_arguments=TRUE)
+opt <- args$options
+
+
+get_num_components = function(components_data)
+{
+    # Get the max of the number_comp column.
+    number_comp = components_data[, 3]
+    num_components <- max(number_comp, na.rm=TRUE);
+    num_components
+}
+
+get_pi_mu_var = function(components_data, num_components)
+{
+    # FixMe: enhance this to generically handle any integer value for num_components.
+    if (num_components == 1)
+    {
+        pi <- c(components_data[1, 9]);
+        mu <- c(components_data[1, 7]);
+        var <- c(components_data[1, 8]);
+    }
+    else if (num_components == 2)
+    {
+        pi <- c(components_data[2, 9], components_data[3, 9]);
+        mu <- c(components_data[2, 7], components_data[3, 7]);
+        var <- c(components_data[2, 8], components_data[3, 8]);
+    }
+    else if (num_components == 3)
+    {
+        pi <- c(components_data[4, 9], components_data[5, 9], components_data[6, 9]);
+        mu <- c(components_data[4, 7], components_data[5, 7], components_data[6, 7]);
+        var <- c(components_data[4, 8], components_data[5, 8], components_data[6, 8]);
+    }
+    else if (num_components == 4)
+    {
+        pi <- c(components_data[7, 9], components_data[8, 9], components_data[9, 9], components_data[10, 9]);
+        mu <- c(components_data[7, 7], components_data[8, 7], components_data[9, 7], components_data[10, 7]);
+        var <- c(components_data[7, 8], components_data[8, 8], components_data[9, 8], components_data[10, 8]);
+    }
+    return = c(pi, mu, var)
+    return
+}
+
+plot_ks<-function(kaks_input, output, pi, mu, var)
+{
+    # Start PDF device driver to save charts to output.
+    pdf(file=output, bg="white")
+    # Change bin width
+    bin <- 0.05 * seq(0, 40);
+    kaks <- read.table(file=kaks_input, header=T);
+    kaks <- kaks[kaks$Ks<2,];
+    h.kst <- hist(kaks$Ks, breaks=bin, plot=F);
+    nc <- h.kst$counts;
+    vx <- h.kst$mids;
+    ntot <- sum(nc);
+    # Set margin for plot bottom, left top, right.
+    par(mai=c(0.5, 0.5, 0, 0));
+    # Plot dimension in inches.
+    par(pin=c(2.5, 2.5));
+    g <- calculate_fitted_density(pi, mu, var);
+    h <- ntot * 2.5 / sum(g);
+    vx <- seq(1, 100) * 0.02;
+    ymax <- max(nc) + 5;
+    barplot(nc, space=0.25, offset=0, width=0.04, xlim=c(0,2), ylim=c(0, ymax));
+    # Add x-axis.
+    axis(1);
+    color <- c('green', 'blue', 'black', 'red');
+    for (i in 1:length(mu))
+    {
+       lines(vx, g[,i] * h, lwd=2, col=color[i]);
+    }
+};
+
+calculate_fitted_density <- function(pi, mu, var)
+{
+    comp <- length(pi);
+    var <- var/mu^2;
+    mu <- log(mu);
+    #calculate lognormal density
+    vx <- seq(1, 100) * 0.02;
+    fx <- matrix(0, 100, comp);
+    for (i in 1:100)
+    {
+        for (j in 1:comp)
+        {
+           fx[i, j] <- pi[j] * dlnorm(vx[i], meanlog=mu[j], sdlog=(sqrt(var[j])));
+        };
+     };
+    fx;
+}
+
+# Read in the components data.
+components_data <- read.delim(opt$components_input, header=TRUE);
+# Get the number of components.
+num_components <- get_num_components(components_data)
+
+# Set pi, mu, var.
+items <- get_pi_mu_var(components_data, num_components);
+pi <- items[1];
+mu <- items[2];
+var <- items[3];
+
+# Plot the output.
+plot_ks(opt$kaks_input, opt$output, pi, mu, var);
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kaks_analysis_distribution.xml	Fri Mar 17 07:47:15 2017 -0400
@@ -0,0 +1,44 @@
+<tool id="kaks_analysis_distribution" name="KaKsAnalysis distribution" version="1.0.0">
+    <description>plots synonymous (ks) distribution and fit significant component</description>
+    <requirements>
+         <requirement type="package" version="1.3.0">r-optparse</requirement>
+    </requirements>
+    <command>
+        <![CDATA[
+            Rscript $__tool_directory__/kaks_analysis_distribution.R
+            -k '${kaks}'
+            -c '${components}'
+            -o '$output'
+        ]]>
+    </command>
+    <inputs>
+        <param name="kaks" format="tabular" type="data" label="KaKs analysis file" />
+        <param name="components" format="tabular" type="data" label="Significant components in the ks distribution" />
+    </inputs>
+    <outputs>
+        <data name="output" format="pdf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="kaks" value="kaks.tabular" ftype="tabular" />
+            <param name="components" value="components.tabular" ftype="tabular" />
+            <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+ 
+Draws a barplot of the significant components in the ks distribution.
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @article{None,
+            journal = {None},
+            author = {1. Wafula EK},
+            title = {Manuscript in preparation},
+            year = {None},
+            url = {https://github.com/dePamphilis/PlantTribes},}
+        </citation>
+    </citations>
+</tool>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/components.tabular	Fri Mar 17 07:47:15 2017 -0400
@@ -0,0 +1,7 @@
+species	n	number_comp	lnL	AIC	BIC	mean	variance	porportion
+species1	1160	1	-1404.9900	2813.98	2824.09	0.4426	0.1293	1.00
+species1	1160	2	-1353.6550	2717.31	2742.59	0.7376	0.1672	0.61
+						0.2000	0.0069	0.39
+species1	1160	3	-1323.7480	2663.50	2703.94	0.1214	0.0002	0.10
+						0.7759	0.1663	0.57
+						0.2428	0.0070	0.33
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kaks.tabular	Fri Mar 17 07:47:15 2017 -0400
@@ -0,0 +1,101 @@
+SEQ1	SEQ2	Ka	Ks	Ka\Ks
+species1_10079	species1_10080	0.1194	0.9782	0.1221
+species1_10818	species1_10817	0.0194	0.9541	0.0203
+species1_4505	species1_4506	0.0379	0.2411	0.1571
+species1_2890	species1_2889	0.0212	0.8520	0.0249
+species1_3386	species1_3385	0.0002	0.1698	0.0010
+species1_2266	species1_2265	0.0881	0.1515	0.5814
+species1_7052	species1_7051	0.0514	0.8172	0.0630
+species1_3374	species1_3373	0.0034	0.4496	0.0075
+species1_688	species1_687	0.1420	0.2970	0.4782
+species1_10669	species1_10670	0.0003	0.3216	0.0010
+species1_9810	species1_9809	0.1490	0.7782	0.1914
+species1_11440	species1_11439	0.0083	0.2177	0.0380
+species1_2713	species1_2714	0.1227	0.2133	0.5755
+species1_4698	species1_4697	0.1021	0.2207	0.4624
+species1_10939	species1_10940	0.0861	0.7844	0.1098
+species1_22	species1_21	0.1368	0.2515	0.5437
+species1_7149	species1_7150	0.0817	0.9899	0.0825
+species1_5139	species1_5140	0.1167	0.2669	0.4373
+species1_3430	species1_3429	0.0803	0.9931	0.0808
+species1_10208	species1_10207	0.0764	0.1098	0.6957
+species1_8410	species1_8409	0.0165	0.8114	0.0204
+species1_2452	species1_2451	0.0629	0.4523	0.1391
+species1_289	species1_290	0.0560	0.1590	0.3526
+species1_10028	species1_10027	0.0927	1.3078	0.0708
+species1_8242	species1_8241	0.0037	0.1390	0.0264
+species1_5661	species1_5662	0.2040	0.5982	0.3410
+species1_85	species1_86	0.0391	0.1012	0.3866
+species1_1660	species1_1659	0.0408	0.3674	0.1111
+species1_616	species1_615	0.0078	0.1315	0.0595
+species1_8043	species1_8044	0.0637	0.3891	0.1637
+species1_1465	species1_1466	0.1186	0.1725	0.6876
+species1_7761	species1_7762	0.2544	0.3513	0.7242
+species1_299	species1_300	0.1407	0.5325	0.2643
+species1_3563	species1_3564	0.0732	0.1679	0.4360
+species1_4847	species1_4848	0.4327	0.6173	0.7009
+species1_3344	species1_3343	0.0642	0.5842	0.1098
+species1_262	species1_261	0.1786	1.5710	0.1137
+species1_3725	species1_3726	0.1883	0.8863	0.2125
+species1_779	species1_780	0.0725	0.2543	0.2849
+species1_1818	species1_1817	0.0681	0.2312	0.2946
+species1_11023	species1_11024	0.1603	0.6655	0.2408
+species1_9653	species1_9654	0.0007	0.7308	0.0010
+species1_6805	species1_6806	0.1090	0.9048	0.1205
+species1_10221	species1_10222	0.0522	0.1314	0.3975
+species1_6011	species1_6012	0.0099	0.9179	0.0108
+species1_5208	species1_5207	0.0931	0.6077	0.1532
+species1_10692	species1_10691	0.0537	0.1868	0.2876
+species1_10036	species1_10035	0.2450	0.4664	0.5254
+species1_1382	species1_1381	0.0682	0.1241	0.5495
+species1_1350	species1_1349	0.0129	0.4414	0.0293
+species1_6889	species1_6890	0.0195	0.7789	0.0251
+species1_4426	species1_4425	0.0399	0.3048	0.1309
+species1_7405	species1_7406	0.0443	1.3004	0.0341
+species1_11014	species1_11013	0.0643	0.9027	0.0712
+species1_8683	species1_8684	0.1321	0.6680	0.1977
+species1_5287	species1_5288	0.0882	0.3480	0.2534
+species1_11671	species1_11672	0.1101	0.2895	0.3802
+species1_551	species1_552	0.0165	0.2045	0.0809
+species1_3396	species1_3395	0.3309	1.6105	0.2055
+species1_5398	species1_5397	0.0004	0.4077	0.0010
+species1_7959	species1_7960	0.0498	0.4343	0.1146
+species1_11030	species1_11029	0.0999	0.2613	0.3825
+species1_10250	species1_10249	0.0486	0.1441	0.3372
+species1_6254	species1_6253	0.6399	0.8894	0.7195
+species1_5438	species1_5437	0.0613	0.2224	0.2757
+species1_5728	species1_5727	0.0788	0.1384	0.5697
+species1_8814	species1_8813	0.1076	1.8253	0.0590
+species1_6351	species1_6352	0.2963	0.8001	0.3704
+species1_11253	species1_11254	0.1359	0.7304	0.1860
+species1_11373	species1_11374	0.0924	0.1261	0.7325
+species1_4903	species1_4904	0.1021	1.3915	0.0734
+species1_4326	species1_4325	0.0275	0.1845	0.1492
+species1_9047	species1_9048	0.0648	2.3728	0.0273
+species1_7487	species1_7488	0.0488	0.2406	0.2029
+species1_1125	species1_1126	0.0813	0.3900	0.2085
+species1_9140	species1_9139	0.1643	0.7126	0.2306
+species1_3355	species1_3356	0.0262	0.9844	0.0266
+species1_7068	species1_7067	0.0368	0.1055	0.3492
+species1_8341	species1_8342	0.0356	0.6112	0.0583
+species1_4871	species1_4872	0.0728	0.2256	0.3227
+species1_4408	species1_4407	0.1148	0.7863	0.1460
+species1_10007	species1_10008	0.1071	0.5462	0.1960
+species1_236	species1_235	0.0834	0.2601	0.3207
+species1_4571	species1_4572	0.0745	1.0106	0.0737
+species1_897	species1_898	0.0916	0.9281	0.0987
+species1_5161	species1_5162	0.0707	0.4099	0.1725
+species1_6899	species1_6900	0.0814	0.6724	0.1210
+species1_5749	species1_5750	0.0325	0.3209	0.1013
+species1_2843	species1_2844	0.0327	0.8263	0.0396
+species1_653	species1_654	0.0382	0.8706	0.0439
+species1_8698	species1_8697	0.2628	2.2612	0.1162
+species1_405	species1_406	0.1135	0.1936	0.5861
+species1_4782	species1_4781	0.0341	1.1289	0.0302
+species1_42	species1_41	0.1711	0.4618	0.3706
+species1_1330	species1_1329	0.1074	0.7932	0.1354
+species1_11127	species1_11128	0.1866	1.6162	0.1155
+species1_7639	species1_7640	0.0787	0.4300	0.1830
+species1_7061	species1_7062	0.0571	0.3851	0.1483
+species1_56	species1_55	0.0260	0.6935	0.0375
+species1_417	species1_418	0.0272	0.8148	0.0334
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.pdf	Fri Mar 17 07:47:15 2017 -0400
@@ -0,0 +1,67 @@
+%PDF-1.4
+%ρ\r
+1 0 obj
+<<
+/Title (R Graphics Output)
+/Creator (R)
+>>
+endobj
+2 0 obj
+<< /Type /Catalog /Pages 3 0 R >>
+endobj
+7 0 obj
+<< /Type /Page /Parent 3 0 R /Contents 8 0 R /Resources 4 0 R >>
+endobj
+8 0 obj
+<<
+/Length 1245 /Filter /FlateDecode
+>>
+stream
+endobj
+3 0 obj
+<< /Type /Pages /Kids [ 7 0 R ] /Count 1 /MediaBox [0 0 504 504] >>
+endobj
+4 0 obj
+<<
+/ProcSet [/PDF /Text]
+/Font <</F2 10 0 R >>
+/ExtGState << >>
+/ColorSpace << /sRGB 5 0 R >>
+>>
+endobj
+5 0 obj
+[/ICCBased 6 0 R]
+endobj
+6 0 obj
+<< /Alternate /DeviceRGB /N 3 /Length 2596 /Filter /FlateDecode >>
+stream
+9 0 obj
+<<
+/Type /Encoding /BaseEncoding /WinAnsiEncoding
+/Differences [ 45/minus 96/quoteleft
+144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent
+/dieresis /.notdef /ring /cedilla /.notdef /hungarumlaut /ogonek /caron /space]
+>>
+endobj
+10 0 obj
+<< /Type /Font /Subtype /Type1 /Name /F2 /BaseFont /Helvetica
+/Encoding 9 0 R >>
+endobj
+xref
+0 11
+0000000000 65535 f 
+0000000021 00000 n 
+0000000163 00000 n 
+0000001609 00000 n 
+0000001692 00000 n 
+0000001804 00000 n 
+0000001837 00000 n 
+0000000212 00000 n 
+0000000292 00000 n 
+0000004532 00000 n 
+0000004789 00000 n 
+trailer
+<< /Size 11 /Info 1 0 R /Root 2 0 R >>
+startxref
+4886
+%%EOF