From 78f6df33c2d1d58ae63a36906b443637be8978c7 Mon Sep 17 00:00:00 2001 From: Cameron Mattson Date: Fri, 13 Dec 2024 14:00:48 -0700 Subject: [PATCH] Fixed typos in pairwise compare notebook --- docs/example_pairwise_comparisons.ipynb | 280 ++++++++++++------------ 1 file changed, 140 insertions(+), 140 deletions(-) diff --git a/docs/example_pairwise_comparisons.ipynb b/docs/example_pairwise_comparisons.ipynb index 8f4ab69..d134784 100644 --- a/docs/example_pairwise_comparisons.ipynb +++ b/docs/example_pairwise_comparisons.ipynb @@ -16,10 +16,10 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2024-12-02T19:52:44.430148Z", - "iopub.status.busy": "2024-12-02T19:52:44.430015Z", - "iopub.status.idle": "2024-12-02T19:52:44.647935Z", - "shell.execute_reply": "2024-12-02T19:52:44.647555Z" + "iopub.execute_input": "2024-12-13T20:58:24.149172Z", + "iopub.status.busy": "2024-12-13T20:58:24.148996Z", + "iopub.status.idle": "2024-12-13T20:58:24.639576Z", + "shell.execute_reply": "2024-12-13T20:58:24.639167Z" }, "jukit_cell_id": "JlHVCFc6jg" }, @@ -45,10 +45,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-12-02T19:52:44.649701Z", - "iopub.status.busy": "2024-12-02T19:52:44.649507Z", - "iopub.status.idle": "2024-12-02T19:52:44.652722Z", - "shell.execute_reply": "2024-12-02T19:52:44.652420Z" + "iopub.execute_input": "2024-12-13T20:58:24.641172Z", + "iopub.status.busy": "2024-12-13T20:58:24.640979Z", + "iopub.status.idle": "2024-12-13T20:58:24.648286Z", + "shell.execute_reply": "2024-12-13T20:58:24.647986Z" }, "jukit_cell_id": "KnQdvFxPkd" }, @@ -72,10 +72,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-12-02T19:52:44.653983Z", - "iopub.status.busy": "2024-12-02T19:52:44.653793Z", - "iopub.status.idle": "2024-12-02T19:52:44.706713Z", - "shell.execute_reply": "2024-12-02T19:52:44.706323Z" + "iopub.execute_input": "2024-12-13T20:58:24.649669Z", + "iopub.status.busy": "2024-12-13T20:58:24.649556Z", + "iopub.status.idle": "2024-12-13T20:58:24.755600Z", + "shell.execute_reply": "2024-12-13T20:58:24.755261Z" }, "jukit_cell_id": "dlU1p2c9cE" }, @@ -102,10 +102,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-12-02T19:52:44.708297Z", - "iopub.status.busy": "2024-12-02T19:52:44.708140Z", - "iopub.status.idle": "2024-12-02T19:52:44.721039Z", - "shell.execute_reply": "2024-12-02T19:52:44.720758Z" + "iopub.execute_input": "2024-12-13T20:58:24.756964Z", + "iopub.status.busy": "2024-12-13T20:58:24.756808Z", + "iopub.status.idle": "2024-12-13T20:58:24.782573Z", + "shell.execute_reply": "2024-12-13T20:58:24.782268Z" }, "jukit_cell_id": "gQ5lHlQ04X" }, @@ -393,10 +393,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2024-12-02T19:52:44.745963Z", - "iopub.status.busy": "2024-12-02T19:52:44.745676Z", - "iopub.status.idle": "2024-12-02T19:52:44.748082Z", - "shell.execute_reply": "2024-12-02T19:52:44.747780Z" + "iopub.execute_input": "2024-12-13T20:58:24.813376Z", + "iopub.status.busy": "2024-12-13T20:58:24.813222Z", + "iopub.status.idle": "2024-12-13T20:58:24.815733Z", + "shell.execute_reply": "2024-12-13T20:58:24.815308Z" }, "jukit_cell_id": "ybX13ZBK8Q" }, @@ -435,7 +435,7 @@ "jukit_cell_id": "6gx14BlSwz" }, "source": [ - "## Compare between wells and siRNA treatments with the same concentration" + "## Compare between different wells and siRNA concentrations" ] }, { @@ -443,10 +443,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2024-12-02T19:52:44.749262Z", - "iopub.status.busy": "2024-12-02T19:52:44.749084Z", - "iopub.status.idle": "2024-12-02T19:53:08.806010Z", - "shell.execute_reply": "2024-12-02T19:53:08.805601Z" + "iopub.execute_input": "2024-12-13T20:58:24.817376Z", + "iopub.status.busy": "2024-12-13T20:58:24.817198Z", + "iopub.status.idle": "2024-12-13T20:58:48.225778Z", + "shell.execute_reply": "2024-12-13T20:58:48.225233Z" }, "jukit_cell_id": "CRa8vLBRj8" }, @@ -469,10 +469,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2024-12-02T19:53:08.807845Z", - "iopub.status.busy": "2024-12-02T19:53:08.807680Z", - "iopub.status.idle": "2024-12-02T19:53:08.812868Z", - "shell.execute_reply": "2024-12-02T19:53:08.812532Z" + "iopub.execute_input": "2024-12-13T20:58:48.227715Z", + "iopub.status.busy": "2024-12-13T20:58:48.227573Z", + "iopub.status.idle": "2024-12-13T20:58:48.233127Z", + "shell.execute_reply": "2024-12-13T20:58:48.232737Z" }, "jukit_cell_id": "cGLOXfXNrN" }, @@ -587,10 +587,10 @@ "execution_count": 8, "metadata": { "execution": { - "iopub.execute_input": "2024-12-02T19:53:08.814179Z", - "iopub.status.busy": "2024-12-02T19:53:08.814037Z", - "iopub.status.idle": "2024-12-02T19:53:08.816150Z", - "shell.execute_reply": "2024-12-02T19:53:08.815814Z" + "iopub.execute_input": "2024-12-13T20:58:48.234569Z", + "iopub.status.busy": "2024-12-13T20:58:48.234289Z", + "iopub.status.idle": "2024-12-13T20:58:48.236737Z", + "shell.execute_reply": "2024-12-13T20:58:48.236350Z" }, "jukit_cell_id": "qzMvL0c8sb" }, @@ -614,10 +614,10 @@ "execution_count": 9, "metadata": { "execution": { - "iopub.execute_input": "2024-12-02T19:53:08.817405Z", - "iopub.status.busy": "2024-12-02T19:53:08.817251Z", - "iopub.status.idle": "2024-12-02T19:53:08.819387Z", - "shell.execute_reply": "2024-12-02T19:53:08.819051Z" + "iopub.execute_input": "2024-12-13T20:58:48.238100Z", + "iopub.status.busy": "2024-12-13T20:58:48.237864Z", + "iopub.status.idle": "2024-12-13T20:58:48.240138Z", + "shell.execute_reply": "2024-12-13T20:58:48.239749Z" }, "jukit_cell_id": "7modF1v2ll" }, @@ -641,7 +641,7 @@ "jukit_cell_id": "ucjifXHnJI" }, "source": [ - "## Compare between different siRNAs and Wells at the same concentrations" + "## Compare between different siRNAs and wells at the same concentrations" ] }, { @@ -649,10 +649,10 @@ "execution_count": 10, "metadata": { "execution": { - "iopub.execute_input": "2024-12-02T19:53:08.820624Z", - "iopub.status.busy": "2024-12-02T19:53:08.820488Z", - "iopub.status.idle": "2024-12-02T19:53:11.115742Z", - "shell.execute_reply": "2024-12-02T19:53:11.115336Z" + "iopub.execute_input": "2024-12-13T20:58:48.241509Z", + "iopub.status.busy": "2024-12-13T20:58:48.241210Z", + "iopub.status.idle": "2024-12-13T20:58:50.438288Z", + "shell.execute_reply": "2024-12-13T20:58:50.437902Z" }, "jukit_cell_id": "JPLwsPbVsU" }, @@ -676,10 +676,10 @@ "execution_count": 11, "metadata": { "execution": { - "iopub.execute_input": "2024-12-02T19:53:11.117480Z", - "iopub.status.busy": "2024-12-02T19:53:11.117341Z", - "iopub.status.idle": "2024-12-02T19:53:11.122848Z", - "shell.execute_reply": "2024-12-02T19:53:11.122493Z" + "iopub.execute_input": "2024-12-13T20:58:50.440204Z", + "iopub.status.busy": "2024-12-13T20:58:50.440051Z", + "iopub.status.idle": "2024-12-13T20:58:50.445450Z", + "shell.execute_reply": "2024-12-13T20:58:50.445122Z" }, "jukit_cell_id": "lFR01EXVLC" }, @@ -708,62 +708,62 @@ " pearsons_correlation\n", " Metadata_Concentration__antehoc_group0\n", " Metadata_Concentration__antehoc_group1\n", - " Metadata_siRNA__posthoc_group0\n", - " Metadata_siRNA__posthoc_group1\n", " Metadata_Well__posthoc_group0\n", " Metadata_Well__posthoc_group1\n", + " Metadata_siRNA__posthoc_group0\n", + " Metadata_siRNA__posthoc_group1\n", " \n", " \n", " \n", " \n", " 0\n", - " 0.128001\n", + " -0.258292\n", " 0.001\n", " 0.001\n", - " NF1 Target 1\n", - " NF1 Target 2\n", + " E10\n", " F10\n", - " G10\n", + " Scramble\n", + " NF1 Target 1\n", " \n", " \n", " 1\n", - " 0.190290\n", + " -0.011791\n", " 0.001\n", " 0.001\n", + " E10\n", + " F4\n", + " Scramble\n", " NF1 Target 1\n", - " NF1 Target 2\n", - " F10\n", - " G4\n", " \n", " \n", " 2\n", - " 0.173737\n", + " 0.188021\n", " 0.001\n", " 0.001\n", + " E10\n", + " F7\n", + " Scramble\n", " NF1 Target 1\n", - " NF1 Target 2\n", - " F10\n", - " G7\n", " \n", " \n", " 3\n", - " -0.258292\n", + " -0.045444\n", " 0.001\n", " 0.001\n", - " NF1 Target 1\n", - " Scramble\n", - " F10\n", " E10\n", + " G10\n", + " Scramble\n", + " NF1 Target 2\n", " \n", " \n", " 4\n", - " 0.089742\n", + " -0.081625\n", " 0.001\n", " 0.001\n", - " NF1 Target 1\n", + " E10\n", + " G4\n", " Scramble\n", - " F10\n", - " E4\n", + " NF1 Target 2\n", " \n", " \n", "\n", @@ -771,32 +771,32 @@ ], "text/plain": [ " pearsons_correlation Metadata_Concentration__antehoc_group0 \\\n", - "0 0.128001 0.001 \n", - "1 0.190290 0.001 \n", - "2 0.173737 0.001 \n", - "3 -0.258292 0.001 \n", - "4 0.089742 0.001 \n", + "0 -0.258292 0.001 \n", + "1 -0.011791 0.001 \n", + "2 0.188021 0.001 \n", + "3 -0.045444 0.001 \n", + "4 -0.081625 0.001 \n", "\n", - " Metadata_Concentration__antehoc_group1 Metadata_siRNA__posthoc_group0 \\\n", - "0 0.001 NF1 Target 1 \n", - "1 0.001 NF1 Target 1 \n", - "2 0.001 NF1 Target 1 \n", - "3 0.001 NF1 Target 1 \n", - "4 0.001 NF1 Target 1 \n", + " Metadata_Concentration__antehoc_group1 Metadata_Well__posthoc_group0 \\\n", + "0 0.001 E10 \n", + "1 0.001 E10 \n", + "2 0.001 E10 \n", + "3 0.001 E10 \n", + "4 0.001 E10 \n", "\n", - " Metadata_siRNA__posthoc_group1 Metadata_Well__posthoc_group0 \\\n", - "0 NF1 Target 2 F10 \n", - "1 NF1 Target 2 F10 \n", - "2 NF1 Target 2 F10 \n", - "3 Scramble F10 \n", - "4 Scramble F10 \n", + " Metadata_Well__posthoc_group1 Metadata_siRNA__posthoc_group0 \\\n", + "0 F10 Scramble \n", + "1 F4 Scramble \n", + "2 F7 Scramble \n", + "3 G10 Scramble \n", + "4 G4 Scramble \n", "\n", - " Metadata_Well__posthoc_group1 \n", - "0 G10 \n", - "1 G4 \n", - "2 G7 \n", - "3 E10 \n", - "4 E4 " + " Metadata_siRNA__posthoc_group1 \n", + "0 NF1 Target 1 \n", + "1 NF1 Target 1 \n", + "2 NF1 Target 1 \n", + "3 NF1 Target 2 \n", + "4 NF1 Target 2 " ] }, "execution_count": 11, @@ -813,10 +813,10 @@ "execution_count": 12, "metadata": { "execution": { - "iopub.execute_input": "2024-12-02T19:53:11.124166Z", - "iopub.status.busy": "2024-12-02T19:53:11.124023Z", - "iopub.status.idle": "2024-12-02T19:53:11.126142Z", - "shell.execute_reply": "2024-12-02T19:53:11.125797Z" + "iopub.execute_input": "2024-12-13T20:58:50.446909Z", + "iopub.status.busy": "2024-12-13T20:58:50.446796Z", + "iopub.status.idle": "2024-12-13T20:58:50.448816Z", + "shell.execute_reply": "2024-12-13T20:58:50.448514Z" }, "jukit_cell_id": "EiRceI8zqd" }, @@ -840,10 +840,10 @@ "execution_count": 13, "metadata": { "execution": { - "iopub.execute_input": "2024-12-02T19:53:11.127483Z", - "iopub.status.busy": "2024-12-02T19:53:11.127297Z", - "iopub.status.idle": "2024-12-02T19:53:11.129395Z", - "shell.execute_reply": "2024-12-02T19:53:11.129049Z" + "iopub.execute_input": "2024-12-13T20:58:50.450152Z", + "iopub.status.busy": "2024-12-13T20:58:50.450027Z", + "iopub.status.idle": "2024-12-13T20:58:50.451967Z", + "shell.execute_reply": "2024-12-13T20:58:50.451666Z" }, "jukit_cell_id": "uHLGwABthL" }, @@ -853,7 +853,7 @@ "output_type": "stream", "text": [ "Output Dataframe Columns:\n", - "['pearsons_correlation', 'Metadata_Concentration__antehoc_group0', 'Metadata_Concentration__antehoc_group1', 'Metadata_siRNA__posthoc_group0', 'Metadata_siRNA__posthoc_group1', 'Metadata_Well__posthoc_group0', 'Metadata_Well__posthoc_group1']\n" + "['pearsons_correlation', 'Metadata_Concentration__antehoc_group0', 'Metadata_Concentration__antehoc_group1', 'Metadata_Well__posthoc_group0', 'Metadata_Well__posthoc_group1', 'Metadata_siRNA__posthoc_group0', 'Metadata_siRNA__posthoc_group1']\n" ] } ], @@ -867,7 +867,7 @@ "jukit_cell_id": "K9KWpg6A7A" }, "source": [ - "## Compare between different stains, conditions, and wells\n", + "## Compare between different siRNAs and wells at the same concentrations\n", "Supplying the _drop_cols parameter excludes wells from the output dataframe, even though wells are used to compare groups." ] }, @@ -876,10 +876,10 @@ "execution_count": 14, "metadata": { "execution": { - "iopub.execute_input": "2024-12-02T19:53:11.130698Z", - "iopub.status.busy": "2024-12-02T19:53:11.130526Z", - "iopub.status.idle": "2024-12-02T19:53:13.372280Z", - "shell.execute_reply": "2024-12-02T19:53:13.371877Z" + "iopub.execute_input": "2024-12-13T20:58:50.453295Z", + "iopub.status.busy": "2024-12-13T20:58:50.453169Z", + "iopub.status.idle": "2024-12-13T20:58:52.612752Z", + "shell.execute_reply": "2024-12-13T20:58:52.612363Z" }, "jukit_cell_id": "OHRc2Dyid6" }, @@ -904,10 +904,10 @@ "execution_count": 15, "metadata": { "execution": { - "iopub.execute_input": "2024-12-02T19:53:13.374236Z", - "iopub.status.busy": "2024-12-02T19:53:13.374071Z", - "iopub.status.idle": "2024-12-02T19:53:13.378578Z", - "shell.execute_reply": "2024-12-02T19:53:13.378233Z" + "iopub.execute_input": "2024-12-13T20:58:52.614565Z", + "iopub.status.busy": "2024-12-13T20:58:52.614438Z", + "iopub.status.idle": "2024-12-13T20:58:52.618560Z", + "shell.execute_reply": "2024-12-13T20:58:52.618237Z" }, "jukit_cell_id": "rGAPBpItug" }, @@ -941,33 +941,33 @@ " \n", " \n", " 0\n", - " 0.128001\n", + " -0.258292\n", + " E10\n", " F10\n", - " G10\n", " \n", " \n", " 1\n", - " 0.190290\n", - " F10\n", - " G4\n", + " -0.011791\n", + " E10\n", + " F4\n", " \n", " \n", " 2\n", - " 0.173737\n", - " F10\n", - " G7\n", + " 0.188021\n", + " E10\n", + " F7\n", " \n", " \n", " 3\n", - " -0.258292\n", - " F10\n", + " -0.045444\n", " E10\n", + " G10\n", " \n", " \n", " 4\n", - " 0.089742\n", - " F10\n", - " E4\n", + " -0.081625\n", + " E10\n", + " G4\n", " \n", " \n", "\n", @@ -975,18 +975,18 @@ ], "text/plain": [ " pearsons_correlation Metadata_Well__posthoc_group0 \\\n", - "0 0.128001 F10 \n", - "1 0.190290 F10 \n", - "2 0.173737 F10 \n", - "3 -0.258292 F10 \n", - "4 0.089742 F10 \n", + "0 -0.258292 E10 \n", + "1 -0.011791 E10 \n", + "2 0.188021 E10 \n", + "3 -0.045444 E10 \n", + "4 -0.081625 E10 \n", "\n", " Metadata_Well__posthoc_group1 \n", - "0 G10 \n", - "1 G4 \n", - "2 G7 \n", - "3 E10 \n", - "4 E4 " + "0 F10 \n", + "1 F4 \n", + "2 F7 \n", + "3 G10 \n", + "4 G4 " ] }, "execution_count": 15, @@ -1003,10 +1003,10 @@ "execution_count": 16, "metadata": { "execution": { - "iopub.execute_input": "2024-12-02T19:53:13.379837Z", - "iopub.status.busy": "2024-12-02T19:53:13.379697Z", - "iopub.status.idle": "2024-12-02T19:53:13.381799Z", - "shell.execute_reply": "2024-12-02T19:53:13.381472Z" + "iopub.execute_input": "2024-12-13T20:58:52.620308Z", + "iopub.status.busy": "2024-12-13T20:58:52.620133Z", + "iopub.status.idle": "2024-12-13T20:58:52.622432Z", + "shell.execute_reply": "2024-12-13T20:58:52.622116Z" }, "jukit_cell_id": "zZHKZyRQcw" }, @@ -1030,10 +1030,10 @@ "execution_count": 17, "metadata": { "execution": { - "iopub.execute_input": "2024-12-02T19:53:13.383054Z", - "iopub.status.busy": "2024-12-02T19:53:13.382878Z", - "iopub.status.idle": "2024-12-02T19:53:13.384941Z", - "shell.execute_reply": "2024-12-02T19:53:13.384609Z" + "iopub.execute_input": "2024-12-13T20:58:52.624091Z", + "iopub.status.busy": "2024-12-13T20:58:52.623907Z", + "iopub.status.idle": "2024-12-13T20:58:52.626160Z", + "shell.execute_reply": "2024-12-13T20:58:52.625845Z" }, "jukit_cell_id": "8G7ZiPRvd8" },