"\u001b[1;32m<ipython-input-39-669ca51bd5a9>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mcovs\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[1;31mNameError\u001b[0m: name 'covs' is not defined"
" gather(key = \"posRelToTSS\", value = \"coverage\", -geneID, -time)\n",
" \n",
"dataGG$posRelToTSS %<>% as.integer()\n",
"\n",
"covs_collapsed <- dataGG %>%\n",
" group_by(time, posRelToTSS) %>%\n",
" summarize(coverageC = mean(coverage))\n",
"print(covs_collapsed)\n",
"\n",
"qplot(posRelToTSS, coverageC, color = time, \n",
" data=covs_collapsed, geom=\"smooth\") "
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Source: local data frame [18,000 x 3]\n",
"Groups: time\n",
"\n",
" time posRelToTSS coverageC\n",
"1 1h 1 1.087838\n",
"2 1h 2 1.094595\n",
"3 1h 3 1.094595\n",
"4 1h 4 1.087838\n",
"5 1h 5 1.101351\n",
"6 1h 6 1.101351\n",
"7 1h 7 1.094595\n",
"8 1h 8 1.087838\n",
"9 1h 9 1.087838\n",
"10 1h 10 1.094595\n",
".. ... ... ...\n"
]
},
{
"output_type": "stream",
"stream": "stderr",
"text": [
"geom_smooth: method=\"auto\" and size of largest group is >=1000, so using gam with formula: y ~ s(x, bs = \"cs\"). Use 'method = x' to change the smoothing method.\n"
"Error in dev.cur(width = 25): unused argument (width = 25)\n"
]
},
{
"output_type": "stream",
"stream": "stderr",
"text": [
"geom_smooth: method=\"auto\" and size of largest group is >=1000, so using gam with formula: y ~ s(x, bs = \"cs\"). Use 'method = x' to change the smoothing method.\n"