diff --git a/201109_Make_records_figure.ipynb b/201109_Make_records_figure.ipynb index 1cbc150..e4fbe0f 100644 --- a/201109_Make_records_figure.ipynb +++ b/201109_Make_records_figure.ipynb @@ -17,7 +17,7 @@ "base_uri": "https://localhost:8080/" }, "id": "nN5hn_S3xlf-", - "outputId": "3454c59f-b0d4-49e9-892c-6324e2066a52" + "outputId": "26b72fb5-bea8-41fa-c853-e0c7a9e52490" }, "outputs": [ { @@ -34,7 +34,7 @@ "import plotnine as p\n", "\n", "%pylab inline\n", - "# %config InlineBackend.figure_formats = ['retina']\n", + "%config InlineBackend.figure_formats = ['retina']\n", "\n", "from datetime import datetime" ] @@ -52,15 +52,6 @@ "data['Reported cells total'] = data['Reported cells total'].str.replace(',', '').map(float)" ] }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": { - "id": "7uPpCE4-xlgE" - }, - "outputs": [], - "source": [] - }, { "cell_type": "code", "execution_count": 3, @@ -69,28 +60,9 @@ }, "outputs": [], "source": [ - "df = data.query('Measurement == \"RNA-seq\"')" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": { - "id": "mwbSk-yYxlgE" - }, - "outputs": [], - "source": [ - "df = df.sort_values('Date')" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": { - "id": "98qekv2txlgE" - }, - "outputs": [], - "source": [ + "df = data.query('Measurement == \"RNA-seq\"').reset_index(drop = True)\n", + "df = df.sort_values('Date')\n", + "\n", "df['Record breaker'] = False\n", "\n", "record = 0\n", @@ -102,19 +74,10 @@ }, { "cell_type": "code", - "execution_count": 5, - "metadata": { - "id": "gKhiRZ8FxlgF" - }, - "outputs": [], - "source": [] - }, - { - "cell_type": "code", - "execution_count": 6, + "execution_count": 4, "metadata": { "id": "Vf8dYAISxlgF", - "outputId": "c1b88b84-b147-47ea-949a-28e947e3dca5", + "outputId": "2e0a1902-d87d-499c-d895-4584343f5051", "colab": { "base_uri": "https://localhost:8080/", "height": 1000 @@ -125,218 +88,218 @@ "output_type": "display_data", "data": { "text/plain": [ - " Shorthand DOI \\\n", - "9 Tang et al NMeth 10.1038/NMETH.1315 \n", - "12 Tang et al CSC 10.1016/j.stem.2010.03.015 \n", - "13 Islam et al GR 10.1101/gr.110882.110 \n", - "17 Hashimshony et al CR 10.1016/j.celrep.2012.08.003 \n", - "24 Yan et al NSMB 10.1038/nsmb.2660 \n", - "30 Islam et al NMeth 10.1038/nmeth.2772 \n", - "31 Deng et al Science 10.1126/science.1245316 \n", - "32 Jaitin et al Science 10.1126/science.1247651 \n", - "33 Soumillon et al bioRxiv 10.1101/003236 \n", - "53 Fan et al Science 10.1126/science.1258367 \n", - "63 Macosko et al Cell 10.1016/j.cell.2015.05.002 \n", - "176 Adamson et al Cell 10.1016/j.cell.2016.11.048 \n", - "178 Dixit et al Cell 10.1016/j.cell.2016.11.038 \n", - "187 Zheng et al NComm 10.1038/ncomms14049 \n", - "311 Han et al Cell 10.1016/j.cell.2018.02.001 \n", - "399 Zeisel et al Cell 10.1016/j.cell.2018.06.021 \n", - "400 Saunders et al Cell 10.1016/j.cell.2018.07.028 \n", - "469 Schmeidel et al Cell 10.1016/j.cell.2018.10.022 \n", - "548 Cao et al Nature 10.1038/s41586-019-0969-x \n", - "579 Rodriques et al Science 10.1126/science.aaw1219 \n", - "1288 Cao et al Science 10.1126/science.aba7721 \n", + " Shorthand DOI \n", + "0 Tang et al NMeth 10.1038/NMETH.1315 \\\n", + "1 Tang et al CSC 10.1016/j.stem.2010.03.015 \n", + "2 Islam et al GR 10.1101/gr.110882.110 \n", + "6 Hashimshony et al CR 10.1016/j.celrep.2012.08.003 \n", + "11 Yan et al NSMB 10.1038/nsmb.2660 \n", + "17 Islam et al NMeth 10.1038/nmeth.2772 \n", + "18 Deng et al Science 10.1126/science.1245316 \n", + "19 Jaitin et al Science 10.1126/science.1247651 \n", + "20 Soumillon et al bioRxiv 10.1101/003236 \n", + "38 Fan et al Science 10.1126/science.1258367 \n", + "48 Macosko et al Cell 10.1016/j.cell.2015.05.002 \n", + "160 Dixit et al Cell 10.1016/j.cell.2016.11.038 \n", + "168 Zheng et al NComm 10.1038/ncomms14049 \n", + "288 Han et al Cell 10.1016/j.cell.2018.02.001 \n", + "373 Saunders et al Cell 10.1016/j.cell.2018.07.028 \n", + "440 Schmeidel et al Cell 10.1016/j.cell.2018.10.022 \n", + "519 Cao et al Nature 10.1038/s41586-019-0969-x \n", + "549 Rodriques et al Science 10.1126/science.aaw1219 \n", + "1223 Cao et al Science 10.1126/science.aba7721 \n", + "1698 Langlieb et al bioRxiv 10.1101/2023.03.06.531307 \n", + "1701 Qiu et al bioRxiv 10.1101/2023.04.05.535726 \n", "\n", - " Authors Journal \\\n", - "9 Fuchou Tang, Catalin Barbacioru, Yangzhou Wang... Nat Methods \n", - "12 Fuchou Tang, Catalin Barbacioru, Siqin Bao, Ca... Cell Stem Cell \n", - "13 S. Islam, U. Kjallquist, A. Moliner, P. Zajac,... Genome Research \n", - "17 Tamar Hashimshony, Florian Wagner, Noa Sher, I... Cell Reports \n", - "24 Liying Yan, Mingyu Yang, Hongshan Guo, Lu Yang... Nat Struct Mol Biol \n", - "30 Saiful Islam, Amit Zeisel, Simon Joost, Gioele... Nat Methods \n", - "31 Q. Deng, D. Ramskold, B. Reinius, R. Sandberg Science \n", - "32 D. A. Jaitin, E. Kenigsberg, H. Keren-Shaul, N... Science \n", - "33 Magali Soumillon, Davide Cacchiarelli, Stefan ... bioRxiv \n", - "53 H. Christina Fan, Glenn K. Fu, Stephen P. A. F... Science \n", - "63 Evan Z. Macosko, Anindita Basu, Rahul Satija, ... Cell \n", - "176 Britt Adamson, Thomas M. Norman, Marco Jost, M... Cell \n", - "178 Atray Dixit, Oren Parnas, Biyu Li, Jenny Chen,... Cell \n", - "187 Grace X. Y. Zheng, Jessica M. Terry, Phillip B... Nat Commun \n", - "311 Xiaoping Han, Renying Wang, Yincong Zhou, Liji... Cell \n", - "399 Amit Zeisel, Hannah Hochgerner, Peter Lönnerbe... Cell \n", - "400 Arpiar Saunders, Evan Z. Macosko, Alec Wysoker... Cell \n", - "469 Benjamin J. Schmiedel, Divya Singh, Ariel Madr... Cell \n", - "548 Junyue Cao, Malte Spielmann, Xiaojie Qiu, Xing... Nature \n", - "579 Samuel G. Rodriques, Robert R. Stickels, Aleks... Science \n", - "1288 Junyue Cao, Diana R. O’Day, Hannah A. Pliner, ... Science \n", + " Authors Journal \n", + "0 Fuchou Tang, Catalin Barbacioru, Yangzhou Wang... Nat Methods \\\n", + "1 Fuchou Tang, Catalin Barbacioru, Siqin Bao, Ca... Cell Stem Cell \n", + "2 S. Islam, U. Kjallquist, A. Moliner, P. Zajac,... Genome Research \n", + "6 Tamar Hashimshony, Florian Wagner, Noa Sher, I... Cell Reports \n", + "11 Liying Yan, Mingyu Yang, Hongshan Guo, Lu Yang... Nat Struct Mol Biol \n", + "17 Saiful Islam, Amit Zeisel, Simon Joost, Gioele... Nat Methods \n", + "18 Q. Deng, D. Ramskold, B. Reinius, R. Sandberg Science \n", + "19 D. A. Jaitin, E. Kenigsberg, H. Keren-Shaul, N... Science \n", + "20 Magali Soumillon, Davide Cacchiarelli, Stefan ... bioRxiv \n", + "38 H. Christina Fan, Glenn K. Fu, Stephen P. A. F... Science \n", + "48 Evan Z. Macosko, Anindita Basu, Rahul Satija, ... Cell \n", + "160 Atray Dixit, Oren Parnas, Biyu Li, Jenny Chen,... Cell \n", + "168 Grace X. Y. Zheng, Jessica M. Terry, Phillip B... Nat Commun \n", + "288 Xiaoping Han, Renying Wang, Yincong Zhou, Liji... Cell \n", + "373 Arpiar Saunders, Evan Z. Macosko, Alec Wysoker... Cell \n", + "440 Benjamin J. Schmiedel, Divya Singh, Ariel Madr... Cell \n", + "519 Junyue Cao, Malte Spielmann, Xiaojie Qiu, Xing... Nature \n", + "549 Samuel G. Rodriques, Robert R. Stickels, Aleks... Science \n", + "1223 Junyue Cao, Diana R. O’Day, Hannah A. Pliner, ... Science \n", + "1698 Jonah Langlieb, Nina Sachdev, Karol Balderrama... bioRxiv \n", + "1701 Chengxiang Qiu, Beth K. Martin, Ian C. Welsh, ... bioRxiv \n", "\n", - " Title Date \\\n", - "9 mRNA-Seq whole-transcriptome analysis of a sin... 2009-04-06 \n", - "12 Tracing the Derivation of Embryonic Stem Cells... 2010-05-07 \n", - "13 Characterization of the single-cell transcript... 2011-05-05 \n", - "17 CEL-Seq: Single-Cell RNA-Seq by Multiplexed Li... 2012-08-30 \n", - "24 Single-cell RNA-Seq profiling of human preimpl... 2013-08-09 \n", - "30 Quantitative single-cell RNA-seq with unique m... 2013-12-22 \n", - "31 Single-Cell RNA-Seq Reveals Dynamic, Random Mo... 2014-01-09 \n", - "32 Massively Parallel Single-Cell RNA-Seq for Mar... 2014-02-14 \n", - "33 Characterization of directed differentiation b... 2014-03-10 \n", - "53 Combinatorial labeling of single cells for gen... 2015-02-05 \n", - "63 Highly Parallel Genome-wide Expression Profili... 2015-05-21 \n", - "176 A Multiplexed Single-Cell CRISPR Screening Pla... 2016-12-15 \n", - "178 Perturb-Seq: Dissecting Molecular Circuits wit... 2016-12-15 \n", - "187 Massively parallel digital transcriptional pro... 2017-01-16 \n", - "311 Mapping the Mouse Cell Atlas by Microwell-Seq 2018-02-23 \n", - "399 Molecular Architecture of the Mouse Nervous Sy... 2018-08-09 \n", - "400 Molecular Diversity and Specializations among ... 2018-08-09 \n", - "469 Impact of Genetic Polymorphisms on Human Immun... 2018-11-15 \n", - "548 The single-cell transcriptional landscape of m... 2019-02-20 \n", - "579 Slide-seq: A scalable technology for measuring... 2019-03-28 \n", - "1288 A human cell atlas of fetal gene expression 2020-11-13 \n", + " Title Date \n", + "0 mRNA-Seq whole-transcriptome analysis of a sin... 2009-04-06 \\\n", + "1 Tracing the Derivation of Embryonic Stem Cells... 2010-05-07 \n", + "2 Characterization of the single-cell transcript... 2011-05-05 \n", + "6 CEL-Seq: Single-Cell RNA-Seq by Multiplexed Li... 2012-08-30 \n", + "11 Single-cell RNA-Seq profiling of human preimpl... 2013-08-09 \n", + "17 Quantitative single-cell RNA-seq with unique m... 2013-12-22 \n", + "18 Single-Cell RNA-Seq Reveals Dynamic, Random Mo... 2014-01-09 \n", + "19 Massively Parallel Single-Cell RNA-Seq for Mar... 2014-02-14 \n", + "20 Characterization of directed differentiation b... 2014-03-10 \n", + "38 Combinatorial labeling of single cells for gen... 2015-02-05 \n", + "48 Highly Parallel Genome-wide Expression Profili... 2015-05-21 \n", + "160 Perturb-Seq: Dissecting Molecular Circuits wit... 2016-12-15 \n", + "168 Massively parallel digital transcriptional pro... 2017-01-16 \n", + "288 Mapping the Mouse Cell Atlas by Microwell-Seq 2018-02-23 \n", + "373 Molecular Diversity and Specializations among ... 2018-08-09 \n", + "440 Impact of Genetic Polymorphisms on Human Immun... 2018-11-15 \n", + "519 The single-cell transcriptional landscape of m... 2019-02-20 \n", + "549 Slide-seq: A scalable technology for measuring... 2019-03-28 \n", + "1223 A human cell atlas of fetal gene expression 2020-11-13 \n", + "1698 The cell type composition of the adult mouse b... 2023-03-08 \n", + "1701 A single-cell transcriptional timelapse of mou... 2023-04-06 \n", "\n", - " bioRxiv DOI Reported cells total Organism \\\n", - "9 - 5.0 Mouse \n", - "12 - 34.0 Mouse \n", - "13 - 85.0 Mouse \n", - "17 - 96.0 C elegans \n", - "24 - 124.0 Human \n", - "30 - 192.0 Mouse \n", - "31 - 269.0 Mouse \n", - "32 - 4468.0 Mouse \n", - "33 10.1101/003236 12832.0 Human \n", - "53 - 15000.0 Human \n", - "63 - 44808.0 Human, Mouse \n", - "176 - 86000.0 Human \n", - "178 - 200000.0 Human, Mouse \n", - "187 10.1101/065912 250000.0 Human, Mouse \n", - "311 - 400000.0 Mouse \n", - "399 10.1101/294918 509876.0 Mouse \n", - "400 10.1101/299081 690000.0 Mouse \n", - "469 NaN 1000000.0 Human \n", - "548 - 2058652.0 Mouse \n", - "579 10.1101/563395 2522640.0 Mouse \n", - "1288 NaN 4062980.0 Human \n", + " bioRxiv DOI Reported cells total Organism \n", + "0 - 5.0 Mouse \\\n", + "1 - 34.0 Mouse \n", + "2 - 85.0 Mouse \n", + "6 - 96.0 C elegans \n", + "11 - 124.0 Human \n", + "17 - 192.0 Mouse \n", + "18 - 269.0 Mouse \n", + "19 - 4468.0 Mouse \n", + "20 10.1101/003236 12832.0 Human \n", + "38 - 15000.0 Human \n", + "48 - 44808.0 Human, Mouse \n", + "160 - 200000.0 Human, Mouse \n", + "168 10.1101/065912 250000.0 Human, Mouse \n", + "288 - 400000.0 Mouse \n", + "373 10.1101/299081 690000.0 Mouse \n", + "440 NaN 1000000.0 Human \n", + "519 - 2058652.0 Mouse \n", + "549 10.1101/563395 2522640.0 Mouse \n", + "1223 NaN 4062980.0 Human \n", + "1698 10.1101/2023.03.06.531307 4388420.0 Mouse \n", + "1701 10.1101/2023.04.05.535726 12400000.0 Mouse \n", "\n", - " Tissue ... Cell clustering \\\n", - "9 Oocyte ... No \n", - "12 Embryo ... NaN \n", - "13 Culture ... Yes \n", - "17 Embryo ... No \n", - "24 Culture ... Yes \n", - "30 Culture ... No \n", - "31 Embryo ... No \n", - "32 Spleen ... Yes \n", - "33 Culture ... NaN \n", - "53 Blood, Culture ... Yes \n", - "63 Eye ... Yes \n", - "176 Culture ... NaN \n", - "178 Culture ... NaN \n", - "187 Blood ... Yes \n", - "311 Bladder, Bone marrow, Brain, Kidney, Liver, Lu... ... NaN \n", - "399 Brain ... Yes \n", - "400 Brain ... Yes \n", - "469 Blood ... NaN \n", - "548 Embryo ... NaN \n", - "579 Brain ... NaN \n", - "1288 Adrenal gland, Brain, Eye, Heart, Intestine, K... ... Yes \n", + " Tissue ... Cell clustering \n", + "0 Oocyte ... No \\\n", + "1 Embryo ... NaN \n", + "2 Culture ... Yes \n", + "6 Embryo ... No \n", + "11 Culture ... Yes \n", + "17 Culture ... No \n", + "18 Embryo ... No \n", + "19 Spleen ... Yes \n", + "20 Culture ... NaN \n", + "38 Blood, Culture ... Yes \n", + "48 Eye ... Yes \n", + "160 Culture ... NaN \n", + "168 Blood ... Yes \n", + "288 Bladder, Bone marrow, Brain, Kidney, Liver, Lu... ... NaN \n", + "373 Brain ... Yes \n", + "440 Blood ... NaN \n", + "519 Embryo ... NaN \n", + "549 Brain ... NaN \n", + "1223 Adrenal gland, Brain, Eye, Heart, Intestine, K... ... Yes \n", + "1698 Brain ... Yes \n", + "1701 NaN ... NaN \n", "\n", - " Pseudotime RNA Velocity PCA tSNE \\\n", - "9 No No No No \n", - "12 NaN No Yes NaN \n", - "13 No NaN Yes No \n", + " Pseudotime RNA Velocity PCA tSNE \n", + "0 No No No No \\\n", + "1 NaN No Yes NaN \n", + "2 No NaN Yes No \n", + "6 No NaN No No \n", + "11 No NaN Yes No \n", "17 No NaN No No \n", - "24 No NaN Yes No \n", - "30 No NaN No No \n", - "31 No No Yes No \n", - "32 No NaN No No \n", - "33 NaN NaN NaN NaN \n", - "53 No NaN Yes No \n", - "63 No No Yes Yes \n", - "176 NaN NaN NaN Yes \n", - "178 NaN NaN NaN No \n", - "187 NaN NaN Yes Yes \n", - "311 NaN NaN NaN NaN \n", - "399 NaN NaN Yes Yes \n", - "400 NaN NaN NaN NaN \n", - "469 NaN NaN NaN NaN \n", - "548 NaN NaN NaN NaN \n", - "579 NaN NaN NaN NaN \n", - "1288 Yes No Yes No \n", + "18 No No Yes No \n", + "19 No NaN No No \n", + "20 NaN NaN NaN NaN \n", + "38 No NaN Yes No \n", + "48 No No Yes Yes \n", + "160 NaN NaN NaN No \n", + "168 NaN NaN Yes Yes \n", + "288 NaN NaN NaN NaN \n", + "373 NaN NaN NaN NaN \n", + "440 NaN NaN NaN NaN \n", + "519 NaN NaN NaN NaN \n", + "549 NaN NaN NaN NaN \n", + "1223 Yes No Yes No \n", + "1698 NaN NaN NaN NaN \n", + "1701 NaN NaN NaN NaN \n", "\n", - " H5AD location \\\n", - "9 NaN \n", - "12 NaN \n", - "13 NaN \n", + " H5AD location \n", + "0 NaN \\\n", + "1 NaN \n", + "2 NaN \n", + "6 NaN \n", + "11 NaN \n", "17 NaN \n", - "24 NaN \n", - "30 NaN \n", - "31 NaN \n", - "32 NaN \n", - "33 NaN \n", - "53 NaN \n", - "63 NaN \n", - "176 NaN \n", - "178 NaN \n", - "187 NaN \n", - "311 NaN \n", - "399 NaN \n", - "400 gs://h5ad/2018-08-Saunders-et-al-Cell \n", - "469 NaN \n", - "548 https://storage.googleapis.com/h5ad/2019-02-Ca... \n", - "579 https://storage.googleapis.com/h5ad/2019-03-Ro... \n", - "1288 https://storage.googleapis.com/h5ad/10.1126-sc... \n", + "18 NaN \n", + "19 NaN \n", + "20 NaN \n", + "38 NaN \n", + "48 NaN \n", + "160 NaN \n", + "168 NaN \n", + "288 NaN \n", + "373 gs://h5ad/2018-08-Saunders-et-al-Cell \n", + "440 NaN \n", + "519 https://storage.googleapis.com/h5ad/2019-02-Ca... \n", + "549 https://storage.googleapis.com/h5ad/2019-03-Ro... \n", + "1223 https://storage.googleapis.com/h5ad/10.1126-sc... \n", + "1698 NaN \n", + "1701 NaN \n", "\n", - " Isolation BC --> Cell ID _OR_ BC --> Cluster ID \\\n", - "9 Pipetting (Manual picking) NaN \n", - "12 NaN NaN \n", - "13 Pipetting (Manual picking) NaN \n", - "17 Pipetting (Manual picking) NaN \n", - "24 NaN NaN \n", - "30 IFC Capture NaN \n", - "31 NaN NaN \n", - "32 Sorting (FACS) NaN \n", - "33 NaN NaN \n", - "53 Picowell deposition NaN \n", - "63 Nanodroplet dilution SCP301 \n", - "176 NaN NaN \n", - "178 Nanodroplet dilution NaN \n", - "187 Nanodroplet dilution NaN \n", - "311 NaN NaN \n", - "399 NaN NaN \n", - "400 NaN NaN \n", - "469 NaN NaN \n", - "548 NaN NaN \n", - "579 Spatial RNA coordinates NaN \n", - "1288 NaN NaN \n", + " Isolation BC --> Cell ID _OR_ BC --> Cluster ID \n", + "0 Pipetting (Manual picking) NaN \\\n", + "1 NaN NaN \n", + "2 Pipetting (Manual picking) NaN \n", + "6 Pipetting (Manual picking) NaN \n", + "11 NaN NaN \n", + "17 IFC Capture NaN \n", + "18 NaN NaN \n", + "19 Sorting (FACS) NaN \n", + "20 NaN NaN \n", + "38 Picowell deposition NaN \n", + "48 Nanodroplet dilution SCP301 \n", + "160 Nanodroplet dilution NaN \n", + "168 Nanodroplet dilution NaN \n", + "288 NaN NaN \n", + "373 NaN NaN \n", + "440 NaN NaN \n", + "519 NaN NaN \n", + "549 Spatial RNA coordinates NaN \n", + "1223 NaN NaN \n", + "1698 NaN NaN \n", + "1701 NaN NaN \n", "\n", - " Number individuals Record breaker \n", - "9 NaN True \n", - "12 NaN True \n", - "13 NaN True \n", - "17 NaN True \n", - "24 NaN True \n", - "30 NaN True \n", - "31 NaN True \n", - "32 NaN True \n", - "33 NaN True \n", - "53 NaN True \n", - "63 NaN True \n", - "176 NaN True \n", - "178 NaN True \n", - "187 NaN True \n", - "311 NaN True \n", - "399 NaN True \n", - "400 NaN True \n", - "469 91.0 True \n", - "548 NaN True \n", - "579 NaN True \n", - "1288 121.0 True \n", + " Number individuals Record breaker \n", + "0 NaN True \n", + "1 NaN True \n", + "2 NaN True \n", + "6 NaN True \n", + "11 NaN True \n", + "17 NaN True \n", + "18 NaN True \n", + "19 NaN True \n", + "20 NaN True \n", + "38 2.0 True \n", + "48 NaN True \n", + "160 NaN True \n", + "168 5.0 True \n", + "288 NaN True \n", + "373 NaN True \n", + "440 91.0 True \n", + "519 NaN True \n", + "549 NaN True \n", + "1223 121.0 True \n", + "1698 NaN True \n", + "1701 NaN True \n", "\n", "[21 rows x 29 columns]" ], "text/html": [ "\n", - "
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