| Previous changeset 0:bdf40b0924cb (2024-02-07) Next changeset 2:d375c9df9c34 (2024-11-07) |
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Commit message:
planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 5e25392164eca5585239b62c82b7f6ba326cda6e |
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modified:
ez_histograms.R ez_histograms.xml test-data/classic.pdf test-data/count.pdf test-data/headless.pdf test-data/large.pdf test-data/rowheadless.pdf test-data/single_headed_col.pdf test-data/summary_1.tsv test-data/summary_2.tsv test-data/summary_3.tsv test-data/summary_4.tsv test-data/summary_5.tsv test-data/summary_6.tsv |
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added:
test-data/misleading_ids.pdf test-data/misleading_ids.tsv test-data/summary_7.tsv |
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| diff -r bdf40b0924cb -r fbedb212982d ez_histograms.R --- a/ez_histograms.R Wed Feb 07 19:49:56 2024 +0000 +++ b/ez_histograms.R Thu Feb 08 02:15:11 2024 +0000 |
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| @@ -2,7 +2,7 @@ library(reshape2) library(dplyr) library(scales) -library(vtable) +library(psych) library(optparse) options(show.error.messages = FALSE, @@ -116,17 +116,9 @@ } } -test_rownames <- function(file) { - data <- read.delim(file = file, header = FALSE, row.names = NULL, nrows = 2) - if (is.na(as.numeric(data[2, 1]))) { - return(1) - } else { - return(NULL) - } -} +##### prepare input data -##### prepare input data -data <- read.delim(file = opt$file, header = test_header(opt$file), row.names = test_rownames(opt$file)) +data <- read.delim(file = opt$file, header = test_header(opt$file)) data <- data %>% select(where(is.numeric)) # remove non numeric columns mdata <- melt(data) @@ -162,8 +154,10 @@ print(p + facet_wrap(~variable, ncol = ncol, scales = "free")) dev.off() -# Summary statistics with vtable package -summary_df <- sumtable(data, digits = 8, out = "return", add.median = TRUE, - summ.names = c("N", "Mean", "Std. Dev.", "Min", "Pctl. 25", - "Median", "Pctl. 75", "Max")) +# Summary statistics with psych package +summary_df <- describe(x = data, skew = FALSE, ranges = FALSE, quant = c(.25, .50, .75)) +summary_df <- cbind(var_names = rownames(summary_df), summary_df) +colnames(summary_df)[2] <- "var_num" +summary_df <- summary_df[, -6] +summary_df[, 4:8] <- format(summary_df[, 4:8], scientific = TRUE) write.table(summary_df, file = opt$summary, sep = "\t", quote = FALSE, row.names = FALSE) |
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| diff -r bdf40b0924cb -r fbedb212982d ez_histograms.xml --- a/ez_histograms.xml Wed Feb 07 19:49:56 2024 +0000 +++ b/ez_histograms.xml Thu Feb 08 02:15:11 2024 +0000 |
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| @@ -1,7 +1,7 @@ <tool id="ez_histograms" name="ez_histograms" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <macros> <token name="@TOOL_VERSION@">3.4.4</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">23.0</token> </macros> <requirements> @@ -9,7 +9,7 @@ <requirement type="package" version="1.4.4">r-reshape2</requirement> <requirement type="package" version="1.1.4">r-dplyr</requirement> <requirement type="package" version="1.3.0">r-scales</requirement> - <requirement type="package" version="1.4.6">r-vtable</requirement> + <requirement type="package" version="2.4.1">r-psych</requirement> <requirement type="package" version="1.7.4">r-optparse</requirement> </requirements> @@ -108,6 +108,13 @@ <output name="pdf" file="single_headed_col.pdf"/> <output name="summary" file="summary_6.tsv"/> </test> + <test expect_num_outputs="2"> + <param name="file" value="misleading_ids.tsv"/> + <param name="plot_options_selector" value="density"/> + <param name="xscale" value="cartesian"/> + <output name="pdf" file="misleading_ids.pdf"/> + <output name="summary" file="summary_7.tsv"/> + </test> </tests> <help><![CDATA[ **What it does** @@ -145,7 +152,7 @@ The ez_histograms Galaxy tool returns - A pdf file with plots faceted on three columns -- A tsv file with statistics summary of the variables generated by the R package vtables +- A tsv file with statistics summary of the variables generated by the R package psych ]]></help> <citations> |
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| diff -r bdf40b0924cb -r fbedb212982d test-data/misleading_ids.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/misleading_ids.tsv Thu Feb 08 02:15:11 2024 +0000 |
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| b'@@ -0,0 +1,1001 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| diff -r bdf40b0924cb -r fbedb212982d test-data/summary_1.tsv --- a/test-data/summary_1.tsv Wed Feb 07 19:49:56 2024 +0000 +++ b/test-data/summary_1.tsv Thu Feb 08 02:15:11 2024 +0000 |
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| @@ -1,7 +1,7 @@ -Variable N Mean Std. Dev. Min Pctl. 25 Median Pctl. 75 Max -BaseMean 990 1091.5132 2625.4763 0 31.199603 249.39264 1054.0101 33915.214 -log2FC 849 -0.38999858 1.9953097 -5.2835189 -2.0088992 -0.86544745 1.2737699 5.6079286 -StdErr 849 0.30667747 0.1285766 0.089282127 0.1962894 0.28928034 0.39630761 0.56482292 -Wald.Stats 849 -0.95820431 6.3140778 -21.603869 -5.9077253 -4.475739 5.2726083 19.585597 -P.value 848 0.030010804 0.15185376 0.00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000016518389 0.0000000000036649168 0.000000012325875 0.0000022785953 0.98727107 -P.adj 813 0.00004223522 0.000078050135 0.0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000034761298 0.000000000255376 0.00000044934286 0.000034873651 0.00028949939 +var_names var_num n mean sd Q0.25 Q0.5 Q0.75 +BaseMean 1 990 1.091513e+03 2.625476e+03 3.119960e+01 2.493926e+02 1.054010e+03 +log2FC 2 849 -3.899986e-01 1.995310e+00 -2.008899e+00 -8.654475e-01 1.273770e+00 +StdErr 3 849 3.066775e-01 1.285766e-01 1.962894e-01 2.892803e-01 3.963076e-01 +Wald.Stats 4 849 -9.582043e-01 6.314078e+00 -5.907725e+00 -4.475739e+00 5.272608e+00 +P.value 5 848 3.001080e-02 1.518538e-01 3.664917e-12 1.232588e-08 2.278595e-06 +P.adj 6 813 4.223522e-05 7.805013e-05 2.553760e-10 4.493429e-07 3.487365e-05 |
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| diff -r bdf40b0924cb -r fbedb212982d test-data/summary_2.tsv --- a/test-data/summary_2.tsv Wed Feb 07 19:49:56 2024 +0000 +++ b/test-data/summary_2.tsv Thu Feb 08 02:15:11 2024 +0000 |
| b |
| @@ -1,16 +1,16 @@ -Variable N Mean Std. Dev. Min Pctl. 25 Median Pctl. 75 Max -GCB_Mg_S2 1000 672.224 1727.7831 0 69 236.5 700 38072 -GCB_Mg_S7 1000 830.225 1848.5916 0 91.5 317 857.25 34261 -GCB_Mg_S12 1000 685.564 1662.1423 0 71 253 686.25 33558 -GCB_S1 1000 450.654 1224.5977 0 38 152 459.5 29464 -GCB_S6 1000 547.793 1344.4334 0 51 194 550 28567 -GCB_S11 1000 481.844 1310.3546 0 40 152.5 462.5 29614 -GW_S5 1000 698.673 1534.1178 0 63.75 237.5 697.75 26119 -GW_S10 1000 573.137 1477.6949 0 49.75 176.5 504 29920 -GW_S15 1000 718.612 1730.7819 0 69 233.5 676 33878 -NS_S4 1000 824.02 1624.4871 0 100 336 914 28284 -NS_S9 1000 704.673 1266.9907 0 93.5 305 796.25 21678 -NS_S14 1000 883.989 1636.9581 0 114.75 366.5 1016 25492 -Starch_S3 1000 905.783 1464.8208 1 135.75 430 1099 22970 -Starch_S8 1000 973.323 1680.7842 0 138.75 426.5 1092.75 24999 -Starch_S13 1000 752.171 1404.0569 0 93 310.5 846.25 22556 +var_names var_num n mean sd Q0.25 Q0.5 Q0.75 +GCB_Mg_S2 1 1000 6.72224e+02 1.727783e+03 6.9000e+01 2.365e+02 7.00000e+02 +GCB_Mg_S7 2 1000 8.30225e+02 1.848592e+03 9.1500e+01 3.170e+02 8.57250e+02 +GCB_Mg_S12 3 1000 6.85564e+02 1.662142e+03 7.1000e+01 2.530e+02 6.86250e+02 +GCB_S1 4 1000 4.50654e+02 1.224598e+03 3.8000e+01 1.520e+02 4.59500e+02 +GCB_S6 5 1000 5.47793e+02 1.344433e+03 5.1000e+01 1.940e+02 5.50000e+02 +GCB_S11 6 1000 4.81844e+02 1.310355e+03 4.0000e+01 1.525e+02 4.62500e+02 +GW_S5 7 1000 6.98673e+02 1.534118e+03 6.3750e+01 2.375e+02 6.97750e+02 +GW_S10 8 1000 5.73137e+02 1.477695e+03 4.9750e+01 1.765e+02 5.04000e+02 +GW_S15 9 1000 7.18612e+02 1.730782e+03 6.9000e+01 2.335e+02 6.76000e+02 +NS_S4 10 1000 8.24020e+02 1.624487e+03 1.0000e+02 3.360e+02 9.14000e+02 +NS_S9 11 1000 7.04673e+02 1.266991e+03 9.3500e+01 3.050e+02 7.96250e+02 +NS_S14 12 1000 8.83989e+02 1.636958e+03 1.1475e+02 3.665e+02 1.01600e+03 +Starch_S3 13 1000 9.05783e+02 1.464821e+03 1.3575e+02 4.300e+02 1.09900e+03 +Starch_S8 14 1000 9.73323e+02 1.680784e+03 1.3875e+02 4.265e+02 1.09275e+03 +Starch_S13 15 1000 7.52171e+02 1.404057e+03 9.3000e+01 3.105e+02 8.46250e+02 |
| b |
| diff -r bdf40b0924cb -r fbedb212982d test-data/summary_3.tsv --- a/test-data/summary_3.tsv Wed Feb 07 19:49:56 2024 +0000 +++ b/test-data/summary_3.tsv Thu Feb 08 02:15:11 2024 +0000 |
| b |
| @@ -1,7 +1,7 @@ -Variable N Mean Std. Dev. Min Pctl. 25 Median Pctl. 75 Max -V2 1000 1286.6999 2744.7392 6.5122425 100.50742 409.92217 1309.8068 33915.214 -V3 1000 -0.4092237 1.9730612 -5.2835189 -2.0884579 -0.946016 1.2600548 5.6079286 -V4 1000 0.30466439 0.1311528 0.089282127 0.19205135 0.28205562 0.40370597 0.56482292 -V5 1000 -0.9419943 6.2085133 -21.603869 -5.7808572 -4.5659907 5.0667272 19.585597 -V6 1000 0.0000018003049 0.000003260254 0.00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000016518389 0.00000000002981881 0.000000042451763 0.0000019035803 0.000013756861 -V7 1000 0.000042996682 0.00007258655 0.0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000034761298 0.0000000025022835 0.000001784909 0.000053393931 0.00028949939 +var_names var_num n mean sd Q0.25 Q0.5 Q0.75 +V2 1 1000 1.286700e+03 2.744739e+03 1.005074e+02 4.099222e+02 1.309807e+03 +V3 2 1000 -4.092237e-01 1.973061e+00 -2.088458e+00 -9.460160e-01 1.260055e+00 +V4 3 1000 3.046644e-01 1.311528e-01 1.920513e-01 2.820556e-01 4.037060e-01 +V5 4 1000 -9.419943e-01 6.208513e+00 -5.780857e+00 -4.565991e+00 5.066727e+00 +V6 5 1000 1.800305e-06 3.260254e-06 2.981881e-11 4.245176e-08 1.903580e-06 +V7 6 1000 4.299668e-05 7.258655e-05 2.502284e-09 1.784909e-06 5.339393e-05 |
| b |
| diff -r bdf40b0924cb -r fbedb212982d test-data/summary_4.tsv --- a/test-data/summary_4.tsv Wed Feb 07 19:49:56 2024 +0000 +++ b/test-data/summary_4.tsv Thu Feb 08 02:15:11 2024 +0000 |
| b |
| b'@@ -1,97 +1,97 @@\n-Variable\tN\tMean\tStd. Dev.\tMin\tPctl. 25\tMedian\tPctl. 75\tMax\n-SC_ph2_46_WT_d0\t1000\t3.11773\t2.1477193\t0\t1.0975\t3.285\t4.7525\t10.19\n-SC_ph2_46_WT_d2\t1000\t3.63747\t2.359001\t0\t1.525\t3.935\t5.33\t12.17\n-SC_ph2_46_WT_d4\t1000\t3.63669\t2.4152548\t0\t1.2475\t3.99\t5.4\t12.17\n-SC_ph2_46_WT_d6\t1000\t3.66312\t2.4765653\t0\t1.08\t4.165\t5.61\t11.72\n-SC_ph2_46_WT_d9\t1000\t3.73941\t2.4700576\t0\t1.33\t4.335\t5.64\t11.77\n-SC_ph2_46_WT_d11\t1000\t3.61458\t2.5333163\t0\t0.95\t4.16\t5.59\t13.31\n-SC_ph2_46_WT_d14\t1000\t3.64982\t2.592493\t0\t0.715\t4.14\t5.6525\t13.62\n-SC_ph2_44_KO_d0\t1000\t3.76101\t2.2973781\t0\t1.9975\t4.065\t5.46\t11.42\n-SC_ph2_44_KO_d2\t1000\t3.63091\t2.39967\t0\t1.37\t3.945\t5.35\t12.17\n-SC_ph2_44_KO_d4\t1000\t3.74617\t2.4163269\t0\t1.4925\t4.105\t5.52\t12.37\n-SC_ph2_44_KO_d6\t1000\t3.77324\t2.3972206\t0\t1.67\t4.245\t5.5925\t11.55\n-SC_ph2_44_KO_d9\t1000\t3.79138\t2.4189072\t0\t1.675\t4.24\t5.5925\t11.58\n-SC_ph2_44_KO_d11\t1000\t3.77987\t2.4282298\t0\t1.715\t4.29\t5.58\t12.36\n-SC_ph2_44_KO_d14\t1000\t3.80486\t2.4590689\t0\t1.44\t4.345\t5.63\t12.76\n-SC_ph2_42_WT_d0\t1000\t3.79097\t2.3332375\t0\t2.0075\t4.13\t5.51\t10.82\n-SC_ph2_42_WT_d2\t1000\t3.61533\t2.3936933\t0\t1.43\t3.945\t5.305\t12.16\n-SC_ph2_42_WT_d4\t1000\t3.66082\t2.4648083\t0\t1.26\t4.015\t5.52\t12.18\n-SC_ph2_42_WT_d6\t1000\t3.70802\t2.4459409\t0\t1.43\t4.2\t5.61\t11.73\n-SC_ph2_42_WT_d9\t1000\t3.78185\t2.4286019\t0\t1.685\t4.25\t5.5925\t11.73\n-SC_ph2_42_WT_d11\t1000\t3.72851\t2.5039993\t0\t1.2075\t4.265\t5.6625\t12.96\n-SC_ph2_42_WT_d14\t1000\t3.75931\t2.5118435\t0\t1.17\t4.255\t5.62\t13.31\n-SC_ph2_20_KO_d0\t1000\t3.08787\t2.117815\t0\t1.2375\t3.22\t4.64\t9.94\n-SC_ph2_20_KO_d4\t1000\t3.66303\t2.4181179\t0\t1.31\t4.08\t5.39\t12.04\n-SC_ph2_20_KO_d6\t1000\t3.66579\t2.4111765\t0\t1.3075\t4.17\t5.53\t11.45\n-SC_ph2_20_KO_d9\t1000\t3.73288\t2.4179454\t0\t1.42\t4.25\t5.55\t11.64\n-SC_ph2_20_KO_d11\t1000\t3.60288\t2.495575\t0\t0.8875\t4.125\t5.52\t13.3\n-SC_ph2_20_KO_d14\t1000\t3.5964\t2.5132892\t0\t0.86\t4.05\t5.48\t13.62\n-SC_wtc11_62_WT_d0\t1000\t3.40212\t2.2730132\t0\t1.3925\t3.665\t5.1025\t9.86\n-SC_wtc11_62_WT_d2\t1000\t3.63876\t2.4205571\t0\t1.44\t4.03\t5.355\t11.8\n-SC_wtc11_62_WT_d4\t1000\t3.64659\t2.4836605\t0\t1.1\t4.035\t5.4925\t11.5\n-SC_wtc11_62_WT_d6\t1000\t3.71569\t2.4669429\t0\t1.4\t4.26\t5.6\t11.35\n-SC_wtc11_62_WT_d9\t1000\t3.80686\t2.4744861\t0\t1.435\t4.345\t5.6825\t11.63\n-SC_wtc11_62_WT_d11\t1000\t3.59131\t2.5337838\t0\t0.8875\t4.05\t5.525\t13.35\n-SC_wtc11_62_WT_d14\t1000\t3.7034\t2.5457967\t0\t0.98\t4.225\t5.59\t13.3\n-SC_wtc11_59_WT_d0\t1000\t3.71923\t2.303389\t0\t1.77\t4.075\t5.48\t11.05\n-SC_wtc11_59_WT_d2\t1000\t3.61826\t2.405514\t0\t1.3875\t3.98\t5.355\t11.73\n-SC_wtc11_59_WT_d4\t1000\t3.64446\t2.4750506\t0\t1.1675\t4.04\t5.53\t12.04\n-SC_wtc11_59_WT_d6\t1000\t3.73685\t2.4738724\t0\t1.2275\t4.285\t5.6025\t11.58\n-SC_wtc11_59_WT_d9\t1000\t3.79347\t2.4629366\t0\t1.425\t4.325\t5.64\t11.71\n-SC_wtc11_59_WT_d11\t1000\t3.8024\t2.4913136\t0\t1.2275\t4.38\t5.66\t12.97\n-SC_wtc11_59_WT_d14\t1000\t3.74929\t2.5130639\t0\t1.1875\t4.195\t5.615\t13.63\n-SC_wtc11_44_KO_d0\t1000\t3.75231\t2.410491\t0\t1.615\t4.09\t5.5225\t11.68\n-SC_wtc11_44_KO_d2\t1000\t3.56306\t2.4033411\t0\t1.2275\t3.855\t5.33\t11.64\n-SC_wtc11_44_KO_d4\t1000\t3.66319\t2.457765\t0\t1.245\t4.06\t5.5125\t11.92\n-SC_wtc11_44_KO_d6\t1000\t3.73555\t2.4341219\t0\t1.3875\t4.215\t5.5625\t11.19\n-SC_wtc11_44_KO_d9\t1000\t3.80402\t2.4530618\t0\t1.44\t4.32\t5.6125\t11.37\n-SC_wtc11_44_KO_d11\t1000\t3.82832\t2.4438198\t0\t1.635\t4.355\t5.61\t12.4\n-SC_wtc11_44_KO_d14\t1000\t3.77796\t2.4686382\t0\t1.39\t4.22\t5.6125\t13.43\n-CBI_NG_5925_d0\t1000\t3.81391\t2.314134\t0\t2.01\t4.115\t5.455\t11.72\n-CBI_NG_5925_d7\t1000\t3.88046\t2.3760604\t0\t1.8975\t4.235\t5.605\t12.15\n-CBI_NG_5925_d14\t1000\t4.03084\t2.3810075\t0\t2.115\t4.485\t5.8\t12.11\n-CBI_NG_5925_d21\t1000\t4.0982\t2.3553707\t0\t2.2275\t4.505\t5.8525\t12.4\n-CBI_NG_5925_d28\t1000\t4.01713\t2.3419343\t0\t2.15\t4.47\t5.73\t12.81\n-CBI_NG_5925_d35\t1000\t4.0037\t2.3726751\t0\t2.095\t4.365\t5.7225\t13\n-CBI_NG_2266_d0\t1000\t3.66515\t2.3917919\t0\t1.6\t3.92\t5.4825\t12.1\n-CBI_NG_2266_d7\t1000\t3.829\t2.3604446\t0\t2\t4.125\t5.53\t12.73\n-CBI_NG_2266_d14\t1000\t3.99827\t2.3516933\t0\t2.1175\t4.42\t5.69\t12.27\n-CBI_NG_2266_d21\t1000\t4.01182\t2.3036996\t0\t2.3475\t4.425\t5.6825\t12.1\n-CBI_NG_2266_d28\t1000\t3.90413\t2.3318045\t0\t1.94\t4.295\t5.57\t12.27\n-CBI_NG_2266_d35\t1000\t3.84252\t2.3786142\t0\t1.7875\t4.235\t5.55'..b'NG_5925_d0\t49\t1000\t3.81391e+00\t2.314134e+00\t2.0100e+00\t4.115e+00\t5.4550e+00\n+CBI_NG_5925_d7\t50\t1000\t3.88046e+00\t2.376060e+00\t1.8975e+00\t4.235e+00\t5.6050e+00\n+CBI_NG_5925_d14\t51\t1000\t4.03084e+00\t2.381007e+00\t2.1150e+00\t4.485e+00\t5.8000e+00\n+CBI_NG_5925_d21\t52\t1000\t4.09820e+00\t2.355371e+00\t2.2275e+00\t4.505e+00\t5.8525e+00\n+CBI_NG_5925_d28\t53\t1000\t4.01713e+00\t2.341934e+00\t2.1500e+00\t4.470e+00\t5.7300e+00\n+CBI_NG_5925_d35\t54\t1000\t4.00370e+00\t2.372675e+00\t2.0950e+00\t4.365e+00\t5.7225e+00\n+CBI_NG_2266_d0\t55\t1000\t3.66515e+00\t2.391792e+00\t1.6000e+00\t3.920e+00\t5.4825e+00\n+CBI_NG_2266_d7\t56\t1000\t3.82900e+00\t2.360445e+00\t2.0000e+00\t4.125e+00\t5.5300e+00\n+CBI_NG_2266_d14\t57\t1000\t3.99827e+00\t2.351693e+00\t2.1175e+00\t4.420e+00\t5.6900e+00\n+CBI_NG_2266_d21\t58\t1000\t4.01182e+00\t2.303700e+00\t2.3475e+00\t4.425e+00\t5.6825e+00\n+CBI_NG_2266_d28\t59\t1000\t3.90413e+00\t2.331804e+00\t1.9400e+00\t4.295e+00\t5.5700e+00\n+CBI_NG_2266_d35\t60\t1000\t3.84252e+00\t2.378614e+00\t1.7875e+00\t4.235e+00\t5.5500e+00\n+CBI_ph2_44_KO_d0\t61\t1000\t3.71693e+00\t2.352512e+00\t1.7375e+00\t3.975e+00\t5.4400e+00\n+CBI_ph2_44_KO_d7\t62\t1000\t3.78661e+00\t2.289096e+00\t2.0950e+00\t4.120e+00\t5.4500e+00\n+CBI_ph2_44_KO_d14\t63\t1000\t4.00159e+00\t2.366675e+00\t2.1375e+00\t4.470e+00\t5.7700e+00\n+CBI_ph2_44_KO_d21\t64\t1000\t4.07712e+00\t2.345013e+00\t2.3475e+00\t4.570e+00\t5.8000e+00\n+CBI_ph2_44_KO_d28\t65\t1000\t3.91843e+00\t2.393440e+00\t2.0175e+00\t4.375e+00\t5.6700e+00\n+CBI_ph2_44_KO_d35\t66\t1000\t3.87058e+00\t2.415086e+00\t1.8675e+00\t4.300e+00\t5.5900e+00\n+CBI_ph2_25_WT_d0\t67\t1000\t3.67504e+00\t2.315179e+00\t1.7075e+00\t3.885e+00\t5.3925e+00\n+CBI_ph2_25_WT_d7\t68\t1000\t3.76218e+00\t2.271138e+00\t2.0075e+00\t4.155e+00\t5.4325e+00\n+CBI_ph2_25_WT_d14\t69\t1000\t3.93884e+00\t2.352815e+00\t2.0650e+00\t4.405e+00\t5.7100e+00\n+CBI_ph2_25_WT_d21\t70\t1000\t4.09695e+00\t2.307157e+00\t2.5100e+00\t4.550e+00\t5.7775e+00\n+CBI_ph2_25_WT_d28\t71\t1000\t3.98384e+00\t2.270183e+00\t2.2675e+00\t4.435e+00\t5.6400e+00\n+CBI_ph2_25_WT_d35\t72\t1000\t3.95099e+00\t2.263501e+00\t2.3775e+00\t4.340e+00\t5.5600e+00\n+CBII_NG_5925_d7\t73\t1000\t3.83078e+00\t2.357625e+00\t1.8975e+00\t4.195e+00\t5.5325e+00\n+CBII_NG_5925_d14\t74\t1000\t3.98798e+00\t2.342508e+00\t2.0950e+00\t4.440e+00\t5.7500e+00\n+CBII_NG_5925_d21\t75\t1000\t4.09168e+00\t2.269262e+00\t2.4400e+00\t4.540e+00\t5.7700e+00\n+CBII_NG_5925_d28\t76\t1000\t4.12182e+00\t2.265089e+00\t2.5975e+00\t4.545e+00\t5.7725e+00\n+CBII_NG_5925_d35\t77\t1000\t4.06331e+00\t2.213558e+00\t2.5900e+00\t4.460e+00\t5.5725e+00\n+CBII_NG_2266_d7\t78\t1000\t3.64617e+00\t2.295589e+00\t1.7825e+00\t3.950e+00\t5.3350e+00\n+CBII_NG_2266_d14\t79\t1000\t3.92017e+00\t2.343534e+00\t1.9850e+00\t4.380e+00\t5.6500e+00\n+CBII_NG_2266_d21\t80\t1000\t3.93792e+00\t2.268592e+00\t2.3200e+00\t4.325e+00\t5.5900e+00\n+CBII_NG_2266_d28\t81\t1000\t3.92191e+00\t2.333792e+00\t2.0800e+00\t4.345e+00\t5.5825e+00\n+CBII_NG_2266_d35\t82\t1000\t3.77144e+00\t2.362880e+00\t1.7825e+00\t4.215e+00\t5.4625e+00\n+CBII_ph2_44_KO_d7\t83\t1000\t3.79221e+00\t2.301786e+00\t1.9175e+00\t4.165e+00\t5.4800e+00\n+CBII_ph2_44_KO_d14\t84\t1000\t3.94071e+00\t2.341508e+00\t2.1100e+00\t4.455e+00\t5.6825e+00\n+CBII_ph2_44_KO_d21\t85\t1000\t3.95096e+00\t2.361846e+00\t2.1450e+00\t4.440e+00\t5.6925e+00\n+CBII_ph2_44_KO_d28\t86\t1000\t3.92924e+00\t2.447976e+00\t1.9150e+00\t4.375e+00\t5.7100e+00\n+CBII_ph2_44_KO_d35\t87\t1000\t3.90667e+00\t2.429660e+00\t1.8250e+00\t4.350e+00\t5.6500e+00\n+CBII_ph2_25_WT_d7\t88\t1000\t3.83587e+00\t2.313905e+00\t2.0125e+00\t4.240e+00\t5.5500e+00\n+CBII_ph2_25_WT_d14\t89\t1000\t3.92400e+00\t2.373410e+00\t1.9850e+00\t4.420e+00\t5.6725e+00\n+CBII_ph2_25_WT_d21\t90\t1000\t4.00121e+00\t2.299976e+00\t2.3225e+00\t4.460e+00\t5.6800e+00\n+CBII_ph2_25_WT_d28\t91\t1000\t4.08491e+00\t2.313130e+00\t2.4050e+00\t4.585e+00\t5.8100e+00\n+CBII_ph2_25_WT_d35\t92\t1000\t3.99314e+00\t2.275504e+00\t2.3025e+00\t4.415e+00\t5.6200e+00\n+CBIII_ph2_25_WT_d14\t93\t1000\t3.84399e+00\t2.321965e+00\t1.8950e+00\t4.290e+00\t5.5625e+00\n+CBIII_ph2_25_WT_d21\t94\t1000\t3.94112e+00\t2.288597e+00\t2.1575e+00\t4.380e+00\t5.6100e+00\n+CBIII_ph2_25_WT_d28\t95\t1000\t4.02923e+00\t2.298249e+00\t2.3500e+00\t4.530e+00\t5.6825e+00\n+CBIII_ph2_25_WT_d35\t96\t1000\t3.98047e+00\t2.267094e+00\t2.3175e+00\t4.440e+00\t5.6775e+00\n' |
| b |
| diff -r bdf40b0924cb -r fbedb212982d test-data/summary_5.tsv --- a/test-data/summary_5.tsv Wed Feb 07 19:49:56 2024 +0000 +++ b/test-data/summary_5.tsv Thu Feb 08 02:15:11 2024 +0000 |
| b |
| @@ -1,7 +1,7 @@ -Variable N Mean Std. Dev. Min Pctl. 25 Median Pctl. 75 Max -V1 1000 1286.6999 2744.7392 6.5122425 100.50742 409.92217 1309.8068 33915.214 -V2 1000 -0.4092237 1.9730612 -5.2835189 -2.0884579 -0.946016 1.2600548 5.6079286 -V3 1000 0.30466439 0.1311528 0.089282127 0.19205135 0.28205562 0.40370597 0.56482292 -V4 1000 -0.9419943 6.2085133 -21.603869 -5.7808572 -4.5659907 5.0667272 19.585597 -V5 1000 0.0000018003049 0.000003260254 0.00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000016518389 0.00000000002981881 0.000000042451763 0.0000019035803 0.000013756861 -V6 1000 0.000042996682 0.00007258655 0.0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000034761298 0.0000000025022835 0.000001784909 0.000053393931 0.00028949939 +var_names var_num n mean sd Q0.25 Q0.5 Q0.75 +V1 1 1000 1.286700e+03 2.744739e+03 1.005074e+02 4.099222e+02 1.309807e+03 +V2 2 1000 -4.092237e-01 1.973061e+00 -2.088458e+00 -9.460160e-01 1.260055e+00 +V3 3 1000 3.046644e-01 1.311528e-01 1.920513e-01 2.820556e-01 4.037060e-01 +V4 4 1000 -9.419943e-01 6.208513e+00 -5.780857e+00 -4.565991e+00 5.066727e+00 +V5 5 1000 1.800305e-06 3.260254e-06 2.981881e-11 4.245176e-08 1.903580e-06 +V6 6 1000 4.299668e-05 7.258655e-05 2.502284e-09 1.784909e-06 5.339393e-05 |
| b |
| diff -r bdf40b0924cb -r fbedb212982d test-data/summary_6.tsv --- a/test-data/summary_6.tsv Wed Feb 07 19:49:56 2024 +0000 +++ b/test-data/summary_6.tsv Thu Feb 08 02:15:11 2024 +0000 |
| b |
| @@ -1,2 +1,2 @@ -Variable N Mean Std. Dev. Min Pctl. 25 Median Pctl. 75 Max -Counts 32833 630.15844 4127.3013 0 0 25 445 552918 +var_names var_num n mean sd Q0.25 Q0.5 Q0.75 +Counts 1 32833 6.301584e+02 4.127301e+03 0e+00 2.5e+01 4.45e+02 |
| b |
| diff -r bdf40b0924cb -r fbedb212982d test-data/summary_7.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary_7.tsv Thu Feb 08 02:15:11 2024 +0000 |
| b |
| @@ -0,0 +1,20 @@ +var_names var_num n mean sd Q0.25 Q0.5 Q0.75 +position 1 1000 1.019385e+03 7.243783e+02 4.715000e+02 8.560000e+02 1.426500e+03 +diff_mod_rate_16h_C2H4_vs_24h_C2H4 2 1000 2.360288e-02 1.348969e-01 -6.518450e-02 3.727249e-02 1.175811e-01 +pval_16h_C2H4_vs_24h_C2H4 3 1000 2.325505e-01 2.381018e-01 5.628020e-02 1.510643e-01 3.110090e-01 +z_score_16h_C2H4_vs_24h_C2H4 4 1000 3.231808e-01 1.644076e+00 -1.172335e+00 7.885085e-01 1.592164e+00 +mod_rate_16h_C2H4.rep0 5 864 6.716916e-01 3.602359e-01 4.824245e-01 8.218392e-01 9.473422e-01 +mod_rate_16h_C2H4.rep1 6 815 6.917358e-01 3.481944e-01 5.610289e-01 8.333017e-01 9.486373e-01 +mod_rate_24h_C2H4.rep0 7 757 6.659981e-01 3.296613e-01 5.175521e-01 7.940631e-01 9.144029e-01 +mod_rate_24h_C2H4.rep1 8 974 6.387455e-01 3.357926e-01 4.619969e-01 7.606182e-01 8.832202e-01 +coverage_16h_C2H4.rep0 9 864 6.813542e+01 1.270829e+02 1.900000e+01 2.800000e+01 5.800000e+01 +coverage_16h_C2H4.rep1 10 815 7.377669e+01 1.426766e+02 1.900000e+01 2.800000e+01 5.300000e+01 +coverage_24h_C2H4.rep0 11 757 8.355218e+01 1.606556e+02 2.000000e+01 3.200000e+01 6.300000e+01 +coverage_24h_C2H4.rep1 12 974 8.322177e+01 1.380622e+02 2.400000e+01 4.000000e+01 7.775000e+01 +mu_unmod 13 1000 9.264596e+01 1.576737e+01 7.965645e+01 8.865965e+01 1.045471e+02 +mu_mod 14 1000 8.783261e+01 1.752936e+01 7.323040e+01 8.370912e+01 1.002537e+02 +sigma2_unmod 15 1000 4.039247e+01 3.492602e+01 1.721010e+01 3.159576e+01 5.172904e+01 +sigma2_mod 16 1000 3.961537e+01 6.321732e+01 8.576091e+00 1.400975e+01 4.034107e+01 +conf_mu_unmod 17 1000 3.981819e-01 3.040734e-01 1.207292e-01 3.337211e-01 6.588437e-01 +conf_mu_mod 18 1000 3.976121e-02 6.878157e-02 1.439629e-03 1.024851e-02 4.468398e-02 +t.tEst 19 1000 9.965072e-02 2.004941e-04 9.948096e-02 9.964975e-02 9.982262e-02 |