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Swarchal/readmap.ipynb

Created September 25, 2018 09:58
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Adding data from a plate-map matrix
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readmap.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th scope=col>V2</th><th scope=col>V3</th><th scope=col>V4</th><th scope=col>V5</th><th scope=col>V6</th><th scope=col>V7</th><th scope=col>V8</th><th scope=col>V9</th><th scope=col>V10</th><th scope=col>V11</th><th scope=col>V12</th><th scope=col>V13</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><td>cond1 </td><td>Cond2 </td><td>Cond10</td><td>Cond18</td><td>Cond26</td><td>Cond34</td><td>Cond42</td><td>Cond50</td><td>Cond58</td><td>Cond66</td><td>Cond74</td><td>cond75</td></tr>\n",
"\t<tr><td>cond1 </td><td>Cond3 </td><td>Cond11</td><td>Cond19</td><td>Cond27</td><td>Cond35</td><td>Cond43</td><td>Cond51</td><td>Cond59</td><td>Cond67</td><td>Cond74</td><td>cond75</td></tr>\n",
"\t<tr><td>cond1 </td><td>Cond4 </td><td>Cond75</td><td>Cond20</td><td>Cond28</td><td>Cond36</td><td>Cond44</td><td>Cond52</td><td>Cond60</td><td>Cond68</td><td>Cond74</td><td>cond75</td></tr>\n",
"\t<tr><td>cond1 </td><td>Cond5 </td><td>Cond13</td><td>Cond21</td><td>Cond29</td><td>Cond37</td><td>Cond45</td><td>Cond53</td><td>Cond61</td><td>Cond69</td><td>Cond74</td><td>cond75</td></tr>\n",
"\t<tr><td>cond1 </td><td>Cond6 </td><td>Cond14</td><td>Cond22</td><td>Cond30</td><td>Cond38</td><td>Cond46</td><td>Cond54</td><td>Cond62</td><td>Cond70</td><td>Cond74</td><td>cond75</td></tr>\n",
"\t<tr><td>cond1 </td><td>Cond7 </td><td>Cond15</td><td>Cond23</td><td>Cond31</td><td>Cond39</td><td>Cond47</td><td>Cond55</td><td>Cond63</td><td>Cond71</td><td>Cond74</td><td>cond75</td></tr>\n",
"\t<tr><td>cond1 </td><td>Cond8 </td><td>Cond16</td><td>Cond24</td><td>Cond32</td><td>Cond40</td><td>Cond48</td><td>Cond56</td><td>Cond64</td><td>Cond72</td><td>Cond74</td><td>cond75</td></tr>\n",
"\t<tr><td>cond1 </td><td>Cond9 </td><td>Cond17</td><td>Cond25</td><td>Cond33</td><td>Cond41</td><td>Cond49</td><td>Cond57</td><td>Cond65</td><td>Cond73</td><td>Cond74</td><td>cond75</td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|llllllllllll}\n",
" V2 & V3 & V4 & V5 & V6 & V7 & V8 & V9 & V10 & V11 & V12 & V13\\\\\n",
"\\hline\n",
"\t cond1 & Cond2 & Cond10 & Cond18 & Cond26 & Cond34 & Cond42 & Cond50 & Cond58 & Cond66 & Cond74 & cond75\\\\\n",
"\t cond1 & Cond3 & Cond11 & Cond19 & Cond27 & Cond35 & Cond43 & Cond51 & Cond59 & Cond67 & Cond74 & cond75\\\\\n",
"\t cond1 & Cond4 & Cond75 & Cond20 & Cond28 & Cond36 & Cond44 & Cond52 & Cond60 & Cond68 & Cond74 & cond75\\\\\n",
"\t cond1 & Cond5 & Cond13 & Cond21 & Cond29 & Cond37 & Cond45 & Cond53 & Cond61 & Cond69 & Cond74 & cond75\\\\\n",
"\t cond1 & Cond6 & Cond14 & Cond22 & Cond30 & Cond38 & Cond46 & Cond54 & Cond62 & Cond70 & Cond74 & cond75\\\\\n",
"\t cond1 & Cond7 & Cond15 & Cond23 & Cond31 & Cond39 & Cond47 & Cond55 & Cond63 & Cond71 & Cond74 & cond75\\\\\n",
"\t cond1 & Cond8 & Cond16 & Cond24 & Cond32 & Cond40 & Cond48 & Cond56 & Cond64 & Cond72 & Cond74 & cond75\\\\\n",
"\t cond1 & Cond9 & Cond17 & Cond25 & Cond33 & Cond41 & Cond49 & Cond57 & Cond65 & Cond73 & Cond74 & cond75\\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"V2 | V3 | V4 | V5 | V6 | V7 | V8 | V9 | V10 | V11 | V12 | V13 | \n",
"|---|---|---|---|---|---|---|---|\n",
"| cond1 | Cond2 | Cond10 | Cond18 | Cond26 | Cond34 | Cond42 | Cond50 | Cond58 | Cond66 | Cond74 | cond75 | \n",
"| cond1 | Cond3 | Cond11 | Cond19 | Cond27 | Cond35 | Cond43 | Cond51 | Cond59 | Cond67 | Cond74 | cond75 | \n",
"| cond1 | Cond4 | Cond75 | Cond20 | Cond28 | Cond36 | Cond44 | Cond52 | Cond60 | Cond68 | Cond74 | cond75 | \n",
"| cond1 | Cond5 | Cond13 | Cond21 | Cond29 | Cond37 | Cond45 | Cond53 | Cond61 | Cond69 | Cond74 | cond75 | \n",
"| cond1 | Cond6 | Cond14 | Cond22 | Cond30 | Cond38 | Cond46 | Cond54 | Cond62 | Cond70 | Cond74 | cond75 | \n",
"| cond1 | Cond7 | Cond15 | Cond23 | Cond31 | Cond39 | Cond47 | Cond55 | Cond63 | Cond71 | Cond74 | cond75 | \n",
"| cond1 | Cond8 | Cond16 | Cond24 | Cond32 | Cond40 | Cond48 | Cond56 | Cond64 | Cond72 | Cond74 | cond75 | \n",
"| cond1 | Cond9 | Cond17 | Cond25 | Cond33 | Cond41 | Cond49 | Cond57 | Cond65 | Cond73 | Cond74 | cond75 | \n",
"\n",
"\n"
],
"text/plain": [
" V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 \n",
"1 cond1 Cond2 Cond10 Cond18 Cond26 Cond34 Cond42 Cond50 Cond58 Cond66 Cond74\n",
"2 cond1 Cond3 Cond11 Cond19 Cond27 Cond35 Cond43 Cond51 Cond59 Cond67 Cond74\n",
"3 cond1 Cond4 Cond75 Cond20 Cond28 Cond36 Cond44 Cond52 Cond60 Cond68 Cond74\n",
"4 cond1 Cond5 Cond13 Cond21 Cond29 Cond37 Cond45 Cond53 Cond61 Cond69 Cond74\n",
"5 cond1 Cond6 Cond14 Cond22 Cond30 Cond38 Cond46 Cond54 Cond62 Cond70 Cond74\n",
"6 cond1 Cond7 Cond15 Cond23 Cond31 Cond39 Cond47 Cond55 Cond63 Cond71 Cond74\n",
"7 cond1 Cond8 Cond16 Cond24 Cond32 Cond40 Cond48 Cond56 Cond64 Cond72 Cond74\n",
"8 cond1 Cond9 Cond17 Cond25 Cond33 Cond41 Cond49 Cond57 Cond65 Cond73 Cond74\n",
" V13 \n",
"1 cond75\n",
"2 cond75\n",
"3 cond75\n",
"4 cond75\n",
"5 cond75\n",
"6 cond75\n",
"7 cond75\n",
"8 cond75"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"library(data.table)\n",
"library(platetools)\n",
"\n",
"# read in data\n",
"# skip the row and column labels\n",
"metadata = fread(\"plate_design.csv\", skip=1, drop=1, header=FALSE)\n",
"metadata"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Create an empty dataframe of just the well labels, or can add these to an existing dataframe."
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th scope=col>well</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><td>A01</td></tr>\n",
"\t<tr><td>A02</td></tr>\n",
"\t<tr><td>A03</td></tr>\n",
"\t<tr><td>A04</td></tr>\n",
"\t<tr><td>A05</td></tr>\n",
"\t<tr><td>A06</td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|l}\n",
" well\\\\\n",
"\\hline\n",
"\t A01\\\\\n",
"\t A02\\\\\n",
"\t A03\\\\\n",
"\t A04\\\\\n",
"\t A05\\\\\n",
"\t A06\\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"well | \n",
"|---|---|---|---|---|---|\n",
"| A01 | \n",
"| A02 | \n",
"| A03 | \n",
"| A04 | \n",
"| A05 | \n",
"| A06 | \n",
"\n",
"\n"
],
"text/plain": [
" well\n",
"1 A01 \n",
"2 A02 \n",
"3 A03 \n",
"4 A04 \n",
"5 A05 \n",
"6 A06 "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"my_data = data.frame(\"well\" = num_to_well(1:96))\n",
"head(my_data)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now you can use the `read_map` function to add data from a matrix to `my_data`."
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th scope=col>well</th><th scope=col>metadata</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><td>A01 </td><td>cond1 </td></tr>\n",
"\t<tr><td>A02 </td><td>Cond2 </td></tr>\n",
"\t<tr><td>A03 </td><td>Cond10</td></tr>\n",
"\t<tr><td>A04 </td><td>Cond18</td></tr>\n",
"\t<tr><td>A05 </td><td>Cond26</td></tr>\n",
"\t<tr><td>A06 </td><td>Cond34</td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|ll}\n",
" well & metadata\\\\\n",
"\\hline\n",
"\t A01 & cond1 \\\\\n",
"\t A02 & Cond2 \\\\\n",
"\t A03 & Cond10\\\\\n",
"\t A04 & Cond18\\\\\n",
"\t A05 & Cond26\\\\\n",
"\t A06 & Cond34\\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"well | metadata | \n",
"|---|---|---|---|---|---|\n",
"| A01 | cond1 | \n",
"| A02 | Cond2 | \n",
"| A03 | Cond10 | \n",
"| A04 | Cond18 | \n",
"| A05 | Cond26 | \n",
"| A06 | Cond34 | \n",
"\n",
"\n"
],
"text/plain": [
" well metadata\n",
"1 A01 cond1 \n",
"2 A02 Cond2 \n",
"3 A03 Cond10 \n",
"4 A04 Cond18 \n",
"5 A05 Cond26 \n",
"6 A06 Cond34 "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"new_data = read_map(my_data, metadata, new_col_name = \"metadata\", verbose=FALSE)\n",
"head(new_data)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "R",
"language": "R",
"name": "ir"
},
"language_info": {
"codemirror_mode": "r",
"file_extension": ".r",
"mimetype": "text/x-r-source",
"name": "R",
"pygments_lexer": "r",
"version": "3.4.4"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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